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Yorodumi- PDB-2x4g: Crystal structure of PA4631, a nucleoside-diphosphate-sugar epime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x4g | ||||||
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Title | Crystal structure of PA4631, a nucleoside-diphosphate-sugar epimerase from Pseudomonas aeruginosa | ||||||
Components | NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / catalytic activity / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Epimerase domain-containing protein Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x4g.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4g.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4g ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4g | HTTPS FTP |
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-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37366.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9HVG0 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE |
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Crystal grow | pH: 8 Details: 2.55M NACL, 0.1M HEPES PH 8 OR 2.9M NACL, 0.1M BICINE PH 8.5 AT A PROTEIN CONCENTRATION OF 2 MG ML-1.CRYSTALS WERE CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 18% GLYCEROL. ...Details: 2.55M NACL, 0.1M HEPES PH 8 OR 2.9M NACL, 0.1M BICINE PH 8.5 AT A PROTEIN CONCENTRATION OF 2 MG ML-1.CRYSTALS WERE CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 18% GLYCEROL. CRYSTAL WAS SOAKED IN 20MM TRIMETHYLLEADCHLORIDE FOR APPROXIMATELY 5 MINUTES BEFORE BEING BACK SOAKED IN CRYO BUFFER |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 21, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→41.7 Å / Num. obs: 12600 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.75 / % possible all: 90 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.65→41.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 23.747 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ORDERED FROM RESIDUES 11 TO 83, 96 TO 280 AND 297 TO 340. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ORDERED FROM RESIDUES 11 TO 83, 96 TO 280 AND 297 TO 340. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.888 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→41.7 Å
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Refine LS restraints |
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