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Yorodumi- PDB-3oa2: Crystal structure of the WlbA (WbpB) dehydrogenase from Pseudomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oa2 | ||||||
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Title | Crystal structure of the WlbA (WbpB) dehydrogenase from Pseudomonas aeruginosa in complex with NAD at 1.5 angstrom resolution | ||||||
Components | WbpB | ||||||
Keywords | OXIDOREDUCTASE / sugar biosynthesis / dehydrogenase | ||||||
Function / homology | Function and homology information UDP-N-acetyl-2-amino-2-deoxyglucuronate dehydrogenase / UDP-glucuronate biosynthetic process / O antigen biosynthetic process / polysaccharide biosynthetic process / NADH binding / lipopolysaccharide biosynthetic process / NADH dehydrogenase activity / protein tetramerization / cell wall organization Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural and Functional Studies of WlbA: A Dehydrogenase Involved in the Biosynthesis of 2,3-Diacetamido-2,3-dideoxy-d-mannuronic Acid . Authors: Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oa2.cif.gz | 277.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oa2.ent.gz | 223.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/3oa2 ftp://data.pdbj.org/pub/pdb/validation_reports/oa/3oa2 | HTTPS FTP |
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-Related structure data
Related structure data | 3o9zSC 3oa0C S: Starting model for refinement 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: 35990.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: wbpB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P72133, UniProt: G3XD23*PLUS #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 298 K / pH: 6.5 Details: 16-22% PEG5000, 2% 1,2-ethanediol, 100 mM PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 206888 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.334 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O9Z Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.568 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.53 Å / Total num. of bins used: 20
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