| 1. |
- Cheeseman, J. D., et al.
(author)
-
Structure of an aryl esterase from Pseudomonas fluorescens
- 2004
-
In: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 60:7, s. 1237-1243
-
Journal article (peer-reviewed)abstract
- The structure of PFE, an aryl esterase from Pseudomonas fluorescens, has been solved to a resolution of 1.8 Å by X-ray diffraction and shows a characteristic α/β-hydrolase fold. In addition to catalyzing the hydrolysis of esters in vitro, PFE also shows low bromoperoxidase activity. PFE shows highest structural similarity, including the active-site environment, to a family of non-heme bacterial haloperoxidases, with an r.m.s. deviation in 271 Cα atoms between PFE and its five closest structural neighbors averaging 0.8 Å. PFE has far less similarity (r.m.s. deviation in 218 Cα atoms of 5.0 Å) to P. fluorescens carboxyl esterase. PFE favors activated esters with small acyl groups, such as phenyl acetate. The X-ray structure of PFE reveals a significantly occluded active site. In addition, several residues, including Trp28 and Met95, limit the size of the acyl-binding pocket, explaining its preference for small acyl groups.
|
|
| 2. |
- Cohen, Serge X., et al.
(author)
-
Towards complete validated models in the next generation of ARP/wARP
- 2004
-
In: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 60:Pt 12 Pt 1, s. 2222-9
-
Journal article (peer-reviewed)abstract
- The design of a new versatile control system that will underlie future releases of the automated model-building package ARP/wARP is presented. A sophisticated expert system is under development that will transform ARP/wARP from a very useful model-building aid to a truly automated package capable of delivering complete, well refined and validated models comparable in quality to the result of intensive manual checking, rebuilding, hypothesis testing, refinement and validation cycles of an experienced crystallographer. In addition to the presentation of this control system, recent advances, ideas and future plans for improving the current model-building algorithms, especially for completing partially built models, are presented. Furthermore, a concept for integrating validation routines into the iterative model-building process is also presented.
|
|
| 3. |
- Dobritzsch, Doreen, 1972-, et al.
(author)
-
Crystallization and preliminary X-ray analysis of beta-alanine synthase from the yeast Saccharomyces kluyveri
- 2003
-
In: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 59:Pt 7, s. 1267-1269
-
Journal article (peer-reviewed)abstract
- In eukaryotes and some bacteria, the third step of reductive pyrimidine catabolism is catalyzed by beta-alanine synthase (EC 3.5.1.6). Crystals of the recombinant enzyme from the yeast Saccharomyces kluyveri were obtained using sodium citrate as a precipitant. The crystals belong to space group P2(1) (unit-cell parameters a = 117.2, b = 77.1, c = 225.5 A, beta = 95.0 degrees ) and contain four homodimers per asymmetric unit. Data were collected to 2.7 A resolution. Introduction of heavy atoms into the crystal lattice induced a different set of unit-cell parameters (a = 61.0, b = 77.9, c = 110.1 A, beta = 97.2 degrees ) in the same space group P2(1), with only one homodimer per asymmetric unit.
|
|
| 4. |
- Dobritzsch, Doreen, 1972-, et al.
(author)
-
Crystallization and preliminary X-ray study of pig liver dihydropyrimidine dehydrogenase
- 2001
-
In: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 57:Pt 1, s. 153-155
-
Journal article (peer-reviewed)abstract
- Dihydropyrimidine dehydrogenase catalyzes the first and rate-limiting reaction in pyrimidine catabolism. The enzyme contains one FMN, one FAD and four Fe-S clusters per subunit of 1025 amino acids as prosthetic groups. It is also the major determinant of bioavailability and toxicity of 5-fluorouracil, a chemotherapeutic agent widely used in the treatment of solid tumors. Crystals of this enzyme diffracting to at least 2.5 A have been obtained by the hanging-drop vapour-diffusion method and belong to space group P2(1) (unit-cell parameters a = 82.0, b = 159.3, c = 163.6 A, beta = 96.1 degrees ), with two homodimers per asymmetric unit.
|
|
| 5. |
- Ekström, Fredrik, 1973-, et al.
(author)
-
Crystallization of the actin-binding domain of human alpha-actinin : analysis of microcrystals of SeMet-labelled protein
- 2003
-
In: Acta Crystallographica Section D. - : Blackwell Munksgaard. - 0907-4449 .- 1399-0047. ; 59:Pt 4, s. 724-726
-
Journal article (peer-reviewed)abstract
- Alpha-actinin forms antiparallel homodimers that cross-link actin filaments from adjacent sarcomeres within the Z-discs of striated muscle. The N-terminal actin-binding domain (ABD) is composed of two calponin homology (CH) domains followed by four spectrin-like repeats and a calmodulin-like EF-hand domain at the C-terminus. The ABD of human alpha-actinin crystallizes in space group P2(1), with unit-cell parameters a = 101.9, b = 38.4, c = 154.9 A, beta = 109.2 degrees. A complete native data set from a native crystal was collected extending to 2.0 A resolution and a single-wavelength anomalous dispersion (SAD) data set to 2.9 A resolution was collected from a selenomethionine-labelled microcrystal using the microfocusing beamline ID-13 at the ESRF. Analysis of the anomalous contribution shows a rapid decrease in the sigma(normal)/sigma(anomal) ratio owing to radiation damage.
|
|
| 6. |
- Grahn, Elin, et al.
(author)
-
Crystallization and preliminary X-ray crystallographic studies of a lectin from the mushroom Marasmius oreades
- 2004
-
In: Acta Crystallographica Section D: Biological Crystallography. - 1399-0047 .- 0907-4449. ; 60:11, s. 2038-2039
-
Journal article (peer-reviewed)abstract
- The Marasmius oreades agglutinin (MOA) recognizes blood group B oligosaccharides. This mushroom lectin belongs to the ricin superfamily and is currently the only lectin known with exclusive specificity for Galα1,3Gal-structures, as occur in the subterminally fucosylated blood group B epitope Galα1,3(Fucα1,2)Galβ1,4GlcNAc (MOA's preferred ligand) or without fucosylation in the xenotransplantation epitope. MOA has been co-crystallized with the linear blood group B trisaccharide Galα1,3Galβ1,4GlcNAc using the hanging-drop vapour-diffusion technique at room temperature. MOA crystals were grown in the presence of ammonium formate and HEPES buffer. A 3.0 Å data set has been collected. Preliminary analysis of the X-ray data is consistent with space group P3 1 or P3 2 and unit-cell parameters a = b = 105, c = 113 Å, with two dimers per asymmetric unit. © 2004 International Union of Crystallography.
|
|
| 7. |
- Hällberg, B. Martin, et al.
(author)
-
Crystallization and preliminary X-ray diffraction analysis of pyranose 2-oxidase from the white-rot fungus Trametes multicolor
- 2004
-
In: Acta Crystallographica Section D. - : International Union of Crystallography (IUCr). - 0907-4449 .- 1399-0047. ; 60, s. 197-199
-
Journal article (peer-reviewed)abstract
- Pyranose 2-oxidase (P2Ox) is a 270 kDa homotetrameric flavoenzyme that catalyzes the oxidation of D-glucose to 2-keto-D-glucose. P2Ox participates in lignin degradation by white-rot fungi and a tentative role of the enzyme is the production of H2O2 for lignin peroxidases. Crystals of Trametes multicolor P2Ox were grown from monomethylether PEG 2000, sodium acetate, MgCl2 and Ta6Br12. They belong to space group P2(1), with unit-cell parameters a = 99.9, b = 101.7, c = 135.6 Angstrom, beta = 90.85degrees. X-ray diffraction data to 2.0 Angstrom resolution were collected using synchrotron radiation. Self-rotation function calculations suggest that the asymmetric unit contains one homotetramer with 222 point-group symmetry.
|
|
| 8. |
- Johansson, P., et al.
(author)
-
Crystallization and preliminary X-ray analysis of a xyloglucan endotransglycosylase from Populus tremula x tremuloides
- 2003
-
In: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 59, s. 535-537
-
Journal article (peer-reviewed)abstract
- Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls. Recombinant XET from poplar has been purified from a Pichia pastoris expression system and crystallized. Two different crystal forms were obtained by vapour diffusion from potassium sodium tartrate and from an imidazole buffer using sodium acetate as a precipitant. Data were collected from these crystal forms to 3.5 and 2.1 Angstrom resolution, respectively. The first crystal form was found to belong to space group P3(1)21 or P3(2)21 (unit-cell parameters a = 98.6, b = 98.6, c = 98.5 Angstrom) and the second crystal form to space group P6(3) (unit-cell parameters a = 188.7, b = 188.7, c = 46.1 Angstrom).
|
|
| 9. |
- Kleywegt, Gerard J, et al.
(author)
-
The Uppsala Electron-Density Server
- 2004
-
In: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 60:Pt 12 Pt 1, s. 2240-2249
-
Journal article (peer-reviewed)abstract
- The Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is a web-based facility that provides access to electron-density maps and statistics concerning the fit of crystal structures and their maps. Maps are available for approximately 87% of the crystallographic Protein Data Bank (PDB) entries for which structure factors have been deposited and for which straightforward map calculations succeed in reproducing the published R value to within five percentage points. Here, an account is provided of the methods that are used to generate the information contained in the server. Some of the problems that are encountered in the map-generation process as well as some spin-offs of the project are also discussed.
|
|
| 10. |
- Knight, Stefan D.
(author)
-
RSPS version 4.0: : a semi-interactive vector-search program for solving heavy-atom derivatives
- 2000
-
In: Acta Crystallographica Section D. - : MUNKSGAARD INT PUBL LTD. - 0907-4449 .- 1399-0047. ; 56:1, s. 42-47
-
Journal article (peer-reviewed)abstract
- A program for inspection and interpretation of the Patterson function is described. The program is mainly intended for finding heavy-atom positions from difference Patterson maps, but may also be used to locate molecules with non-crystallographic symmetry when the local axis is nearly parallel to a crystallographic symmetry axis. Options are available for vector-based methods to locate heavy-atom sites, for finding sets from a list of possible heavy-atom positions and for checking of potential solutions. Both crystallographic and non-crystallographic symmetry may be used, either independently or in conjunction.
|
|
| 11. |
- Meining, Winfried, et al.
(author)
-
Crystallization and preliminary crystallographic analysis of the recombinant N-terminal domain of riboflavin synthase
- 2001
-
In: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 57, s. 1296-1299
-
Journal article (peer-reviewed)abstract
- Riboflavin synthase catalyzes the final step in the biosynthesis of riboflavin. Animals and humans lack this enzyme, whereas many bacteria and certain yeasts are absolutely dependent on endogenous riboflavin synthesis. Riboflavin synthase is therefore an attractive target for chemotherapy. The N-terminal domain of riboflavin synthase forms a dimer in solution and is capable of strongly binding riboflavin. It can serve as a model for the binding site of the native enzyme. Structural information obtained from this domain at high resolution will be helpful in the determination of the binding mode of riboflavin and thus for the development of antimicrobial drugs. Here, the crystallization and preliminary crystallographic analysis of the N-terminal domain of riboflavin synthase are reported. The crystals belong to the space group C222(1), with unit-cell parameters a = 50.3, b = 104.7, c = 85.3 Angstrom, alpha = beta = gamma = 90 degrees, and diffract to 2.6 Angstrom resolution.
|
|
| 12. |
- Oswald, Christine, et al.
(author)
-
Crystallization and preliminary crystallographic analysis of the NAD(H)-binding domain of Escherichia coli transhydrogenase
- 2004
-
In: Acta Crystallographica Section D: Biological Crystallography. - 1399-0047 .- 0907-4449. ; 60:4, s. 743-745
-
Journal article (peer-reviewed)abstract
- Transhydrogenase is a proton-pumping membrane protein that is required for the cellular regeneration of NADPH. The NAD(H)-binding domain (domain I) of transhydrogenase from Escherichia coli was crystallized using the hanging-drop vapour-diffusion technique at room temperature. The crystals, which were grown from PEG 4000 and ammonium acetate in citrate buffer, belong to the triclinic space group P1, with unit-cell parameters a = 38.8, b = 66.8, c = 76.4 Å, α = 67.5, β = 80.8, γ = 81.5°. X-ray diffraction data were collected to 1.9 Å resolution using synchrotron radiation. The crystals contain one dimer of transhydrogenase domain I per asymmetric unit. © 2004 International Union of Crystallography. Printed in Denmark - all rights reserved.
|
|
| 13. |
|
|
| 14. |
|
|
| 15. |
- Andersson, B, et al.
(author)
-
Crystallization and X-ray diffraction data analysis of leukotriene A4 hydrolase from Saccharomyces cerevisiae
- 2003
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; D59:Pt 6, s. 1093-1095
-
Journal article (peer-reviewed)abstract
- The Saccharomyces cerevisiae leukotriene A4 (LTA4) hydrolase (scLTA4 hydrolase) has been crystallized in order to study the two activities of LTA4 hydrolase in an evolutionary perspective. Single well diffracting crystals are obtained after switching from the hanging-drop method to liquid-liquid diffusion in capillaries using PEG 8000 as precipitant. These crystals belong to space group P212121, with unit-cell parameters a = 70.8, b = 98.1, c = 99.2 Å. Intensity data to 2.3 Å resolution were collected from a native scLTA4 hydrolase crystal using synchrotron radiation. A molecular-replacement solution was obtained using the human LTA4 hydrolase structure and the program BEAST.
|
|
| 16. |
- Bakhtiar, Shahrzad, et al.
(author)
-
Crystallization and preliminary X-ray analysis of an alkaline serine protease from Nesterenkonia sp. Acta
- 2003
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 59:3, s. 529-531
-
Journal article (peer-reviewed)abstract
- A novel calcium-independent serine protease from an alkaliphilic bacterium, Nesterenkonia sp. AL20, has been purified and crystallized at 296 K using sodium formate as the main precipitant. This enzyme is optimally active at pH 10, exhibits high stability towards autolytic digestion and its stability is not affected by the presence of EDTA or detergents. The triangular prism-shaped crystals diffracted X-rays to beyond 1.5 Å at a synchrotron beamline, with space group R3 and unit-cell parameters a = b = 92.26, c = 137.88 Å. A complete data set has been collected to 1.39 Å resolution. The asymmetric unit is estimated and confirmed by self-rotation function calculation to contain two molecules, giving a crystal volume per protein mass (VM) of 2.68 Å3 Da-1 and a solvent content of 54%.
|
|
| 17. |
|
|
| 18. |
- Bäckström, Stefan, et al.
(author)
-
Crystallization and preliminary studies of the DNA-binding runt domain of AML1.
- 2001
-
In: Acta Crystallogr D Biol Crystallogr. - 0907-4449. ; 57:Pt 2, s. 269-71
-
Journal article (peer-reviewed)abstract
- The acute myeloid leukaemia 1 (AML1) protein belongs to the Runx family of transcription factors and is crucial for haematopoietic development. The genes encoding Runx1 and its associated factor CBF beta are the most frequent targets for chromosomal rearrangements in acute human leukaemias. In addition, point mutations of Runx1 in acute leukaemias and in the familial platelet disorder FPD/AML cluster within the evolutionary conserved runt domain that binds both DNA and CBF beta. Here, the crystallization of the Runx1 runt domain is reported. Crystals belong to space groups C2 and R32 and diffract to 1.7 and 2.0 A resolution, respectively.
|
|
| 19. |
- Ding, HT, et al.
(author)
-
Parallel cloning, expression, purification and crystallization of human proteins for structural genomics
- 2002
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 58, s. 2102-2108
-
Journal article (peer-reviewed)abstract
- 54 human genes were selected as test targets for parallel cloning, expression, purification and crystallization. Proteins from these genes were selected to have a molecular weight of between 14 and 50 kDa, not to have a high percentage of hydrophobic residues (i.e. more likely to be soluble) and to have no known crystal structures and were not known to be subunits of heterocomplexes. Four proteins containing transmembrane regions were selected for comparative tests. To date, 44 expression clones have been constructed with the Gateway(TM) cloning system (Invitrogen, The Netherlands). Of these, 35 clones were expressed as recombinant proteins in Escherichia coli strain BL21 (DE3)-pLysS, of which 12 were soluble and four have been purified to homogeneity. Crystallization conditions were screened for the purified proteins in 96-well plates under oil. After further refinement with the same device or by the hanging-drop method, crystals were grown, with needle, plate and prism shapes. A 2.12 Angstrom data set was collected for protein NCC27. The results provide insights into the high-throughput target selection, cloning, expression and crystallization of human genomic proteins.
|
|
| 20. |
|
|
| 21. |
|
|
| 22. |
|
|
| 23. |
- Ekström, Fredrik, et al.
(author)
-
Crystallization and X-ray analysis of a bacterial non-haem iron-containing phenylalanine hydroxylase from the Gram-negative opportunistic pathogen Pseudomonas aeruginosa.
- 2003
-
In: Acta Crystallogr D Biol Crystallogr. - 0907-4449. ; 59:Pt 7, s. 1310-2
-
Journal article (peer-reviewed)abstract
- Monooxygenases are frequently involved in the pathways that mediate the pivotal role of microorganisms in recycling carbon from the environment. A structural study of a monooxygenase from Pseudomonas aeruginosa that was identified as a phenylalanine hydroxylase has been initiated. The single-domain monomeric protein harbours a non-haem iron at the active site. The sequence identity to the catalytic domains of tyrosine and tryptophan hydroxylases suggests that the enzyme is not restricted to the substrate phenylalanine alone. Here, the cloning, purification and crystallization of native and SeMet-labelled P. aeruginosa phenylalanine hydroxylase are reported. Crystals grew in space group P6(1), with unit-cell parameters a = b = 210.5, c = 100.7 A, and diffracted to a d spacing of 2.0 A. Crystals of SeMet-labelled protein were used to collect a three-wavelength multiple anomalous dispersion (MAD) data set around the Se K edge.
|
|
| 24. |
- Fedorov, R V, et al.
(author)
-
Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins
- 2001
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; D57:7, s. 968-976
-
Journal article (peer-reviewed)abstract
- The crystal structure of Thermus thermophilus ribosomal protein TL5 in complex with a fragment of Escherichia coli 5S rRNA has been determined at 2.3 Å resolution. The protein consists of two domains. The structure of the N-terminal domain is close to the structure of E. coli ribosomal protein L25, but the C-terminal domain represents a new fold composed of seven -strands connected by long loops. TL5 binds to the RNA through its N-terminal domain, whereas the C-terminal domain is not included in this interaction. Cd2+ ions, the presence of which improved the crystal quality significantly, bind only to the protein component of the complex and stabilize the protein molecule itself and the interactions between the two molecules in the asymmetric unit of the crystal. The TL5 sequence reveals homology to the so-called general stress protein CTC. The hydrophobic cores which stabilize both TL5 domains are highly conserved in CTC proteins. Thus, all CTC proteins may fold with a topology close to that of TL5.
|
|
| 25. |
- Gariani, Talal, et al.
(author)
-
Crystallization and preliminary X-ray diffraction studies of the signal recognition particle receptor FtsY from Mycoplasma mycoides.
- 2000
-
In: Acta Crystallogr D Biol Crystallogr. - 0907-4449. ; 56:Pt 8, s. 1030-2
-
Journal article (peer-reviewed)abstract
- The prokaryotic signal recognition particle (SRP) pathway comprises two proteins, Ffh and FtsY, homologous to the SRP54 and SRalpha proteins in the more complex eukaryotic system. All four proteins are part of a unique subfamily of GTPases. Four truncated versions of the 412 amino-acid FtsY receptor protein from Mycoplasma mycoides have been cloned, expressed in Escherichia coli and purified. Purified proteins from all constructs and the full-length FtsY protein were subjected to crystallization trials. Crystals were obtained for the construct which comprised residues 98-412 corresponding to the conserved NG-domain (residues 194-497 in E. coli). A native data set at 1.9 A resolution has been collected at 100 K using synchrotron radiation. The crystals belong to the space group P2(1)2(1)2, with unit-cell parameters a = 68.7, b = 101.1, c = 42.5 A and one molecule in the asymmetric unit.
|
|
| 26. |
- González, A, et al.
(author)
-
Atomic resolution structure of Escherichia coli dUTPase determined ab initio
- 2001
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 57:Part 6, s. 767-774
-
Journal article (peer-reviewed)abstract
- Cryocooled crystals of a mercury complex of Escherichia coli dUTPase diffract to atomic resolution. Data to 1.05 Å resolution were collected from a derivative crystal and the structure model was derived from a Fourier map with phases calculated from the coordinates of the Hg atom (one site per subunit of the trimeric enzyme) using the program ARP/wARP. After refinement with anisotropic temperature factors a highly accurate model of the bacterial dUTPase was obtained. Data to 1.45 Å from a native crystal were also collected and the 100 K structures were compared. Inspection of the refined models reveals that a large part of the dUTPase remains rather mobile upon freezing, with 14% of the main chain being totally disordered and with numerous side chains containing disordered atoms in multiple discrete conformations. A large number of those residues surround the active-site cavity. Two glycerol molecules (the cryosolvent) occupy the deoxyribose-binding site. Comparison between the native enzyme and the mercury complex shows that the active site is not adversely affected by the binding of mercury. An unexpected effect seems to be a stabilization of the crystal lattice by means of long-range interactions, making derivatization a potentially useful tool for further studies of inhibitor-substrate-analogue complexes of this protein at very high resolution.
|
|
| 27. |
- Guan, Z, et al.
(author)
-
Preparation and crystallization of a Bacillus subtilis arsenate reductase
- 2001
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; D57, s. 1718-1721
-
Journal article (peer-reviewed)abstract
- Arsenate reductase (AR) in B. subtilis is encoded by the chromosomal arsC gene. Together with arsB and arsR, arsC participates in detoxification processes for the arsenate and arsenite ions. Full-length arsenate reductase without any modification has been expressed in Escherichia coli and purified in a soluble form. The recombinant protein has been crystallized at 277 K using polyethyleneglycol (PEG) or poly(ethyleneglycol) methyl ether (PME) as the main precipitant. At least two forms of crystals large enough for data collection have been obtained from wild-type protein under different conditions. An orthorhombic crystal diffracted to beyond 2.2 Å with space group P212121 and unit-cell parameters a = 51.22, b = 91.62, c = 101.93 Å. A near-complete data set has been collected to 2.5 Å. The application of the flash-annealing technique was crucial for high resolution during the data collection. The SeMet-substituted AR has also been produced and crystallized under very similar conditions as the wild type, but the unit-cell parameters are very different. The crystals of the SeMet protein diffracted to higher resolution than those of the wild type.
|
|
| 28. |
- Hakansson, KO, et al.
(author)
-
The three-dimensional structure of catalase from Enterococcus faecalis
- 2004
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 60, s. 1374-1380
-
Journal article (peer-reviewed)abstract
- Enterococcus faecalis haem catalase was crystallized using lithium sulfate at neutral pH. The crystals belong to space group R3, with unit-cell parameters a = b = 236.9, c = 198.1 Angstrom. The three-dimensional structure was determined by molecular replacement using a subunit of the Proteus mirabilis catalase structure. It was refined against 2.3 Angstrom synchrotron data to a free R factor of 21.8%. Like other catalases, the E. faecalis catalase is a homotetramer with a fold and structure similar to those of its structurally closest relative P. mirabilis. The solvent structure in the active site is identical in the four subunits but differs from that found in other catalases. The structural consequences of the Ramachandran outlier Ser196 are discussed.
|
|
| 29. |
- Harris, M, et al.
(author)
-
Molray - a web interface between O and the POV-Ray ray tracer
- 2001
-
In: ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY. - : MUNKSGAARD INT PUBL LTD. - 0907-4449. ; 57, s. 1201-1203
-
Journal article (peer-reviewed)abstract
- A publicly available web-based interface is presented for producing high-quality ray-traced images and movies from the molecular-modelling program O [Jones et al. (1991), Acta Cryst. A47, 110-119]. The interface allows the user to select O-plot files and
|
|
| 30. |
|
|
| 31. |
|
|
| 32. |
|
|
| 33. |
|
|
| 34. |
|
|
| 35. |
|
|
| 36. |
|
|
| 37. |
- Kristensen, Ole, et al.
(author)
-
Crystallization of a stringent response factor from Aquifex aeolicus.
- 2002
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 58:Pt 7, s. 1198-1200
-
Journal article (peer-reviewed)abstract
- The crystallization of a key enzyme from Aquifex aeolicus with suggested bifunctional activity, acting as an exopolyphosphatase and a guanosine pentaphosphate phosphohydrolase, is reported. Native data were collected to below 2 A resolution from an orthorhombic crystal with unit-cell parameters a = 50.8, b = 70.3, c = 90.9 A. Methionine residues were introduced by mutation and deliberate oxidation of the protein allowed us to produce additional crystal forms with reproducible diffraction ability and increased phasing potential. This is the first report on the crystallization of a member of the Ppx/GppA phosphatase family.
|
|
| 38. |
- Kristensen, Ole, et al.
(author)
-
Expression, refolding and crystallization of Aquifex aeolicus elongation factor P.
- 2002
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; D58:Pt 6 Nr 2, s. 1039-1041
-
Journal article (peer-reviewed)abstract
- Elongation factor P is a universally conserved protein stimulating peptidyltransferase activity during protein synthesis. The factor is sensitive to classical inhibitors of the ribosomal peptidyltransferase activity and is possibly involved in alignment of the substrate tRNAs in the catalytic centre of 70S ribosomes. Elongation factor P from the thermophilic Aquifex aeolicus was overexpressed as a soluble protein in Escherichia coli and crystallized. A fast generally applicable refolding protocol was developed to improve crystal quality and circumvent strong binding of oligonucleotides to the protein. Diffraction data collected to 2.7 A resolution present twinning.
|
|
| 39. |
- Lahiri, SD, et al.
(author)
-
Crystallization and preliminary X-ray diffraction studies of beta-phosphoglucomutase from Lactococcus lactus
- 2002
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 58, s. 324-326
-
Journal article (peer-reviewed)abstract
- beta-Phosphoglucomutase (beta-PGM), a 28 kDa monomer, catalyzes the reversible conversion of beta-D-glucose-1-phosphate to beta-D-glucose-6-phosphate in maltose metabolism in a variety of organisms. Sequence analysis of beta-PGM indicates that it is a member of the haloacid dehalogenase (HAD) enzyme superfamily, which evolved to cleave C-Cl, C-P and C-OP bonds in a variety of substrates. beta-PGM has been crystallized using the hanging-drop method. Diffraction-quality crystals of the native protein have been obtained from two conditions, both belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 53.67, b = 92.78, c = 111.60 and a = 53.21, b = 57.01, c = 76.11 Angstrom. To solve the phase problem, selenomethionine (SeMet) containing alpha-PGM crystals have been grown. The SeMet-containing crystals diffract to high resolution only when grown by microseeding with native crystals. A three-wavelength data set has been collected to 2.3 Angstrom on crystals of the SeMet-substituted beta-PGM. The structure solution is currently being attempted by the multi-wavelength anomalous diffraction (MAD) phasing method.
|
|
| 40. |
|
|
| 41. |
|
|
| 42. |
|
|
| 43. |
- Nilsson, Kristina, et al.
(author)
-
An automatic method to generate force-field parameters for hetero-compounds.
- 2003
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 59:2, s. 274-289
-
Journal article (peer-reviewed)abstract
- A method has been developed that automatically constructs a crystallographic refinement force field (topology and parameter files) for any molecule from a theoretical frequency calculation. The approach has been tested on five proteins containing metal sites or non-standard inhibitors or coenzymes and it is shown that the structures are improved in various aspects.
|
|
| 44. |
|
|
| 45. |
- Rudolph, MG, et al.
(author)
-
Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the gamma delta T-cell ligand T10
- 2004
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 60:4, s. 656-664
-
Journal article (peer-reviewed)abstract
- T10 is a non-classical class Ib-like major histocompatibility complex (MHC) cell-surface antigen which binds directly to certain gammadelta T-cell receptors in the absence of any exogenous and endogenous ligands, such as peculiar lipids or glycolipids. The crystal structure at 2.5 Angstrom resolution of murine T10 was determined by molecular replacement using data from an almost perfectly twinned monoclinic crystal. The space group is P2(1), with unit-cell parameters a=78.2, b=70.0, c=139.2 Angstrom, beta=106.8degrees. Self-rotation function analysis and various intensity statistics revealed the presence of pseudo-merohedral twinning, but these tests underestimated the true twin fraction of alphasimilar or equal to0.46. Native Patterson analyses pointed to the presence of pseudo-translation among the four molecules present in the asymmetric unit. Data analysis, structure determination and model refinement are discussed.
|
|
| 46. |
|
|
| 47. |
- Selmer, Maria, et al.
(author)
-
Preparation of a crystallizable mRNA-binding fragment of Moorella thermoacetica elongation factor SelB
- 2002
-
In: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 58, s. 1871-1873
-
Journal article (peer-reviewed)abstract
- SelB is a bacterial elongation factor required for the decoding of a UGA stop codon together with a specific mRNA hairpin to selenocysteine. In attempts to crystallize Moorella thermoacetica SelB, a proteolysis process occurred and crystals of a proteolytic fragment were observed. The crystals, which appeared after a year, contained a C-terminal 30 kDa fragment containing the mRNA-binding domain. This fragment was reproduced through recloning. Crystals diffracting to 2.7 Angstrom were obtained.
|
|
| 48. |
|
|
| 49. |
|
|
| 50. |
|
|
