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Yorodumi- PDB-3o9z: Crystal structure of the WlbA (WbpB) dehydrogenase from Thermus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o9z | ||||||
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Title | Crystal structure of the WlbA (WbpB) dehydrogenase from Thermus thermophilus in complex with NAD and alpha-ketoglutarate at 1.45 angstrom resolution | ||||||
Components | Lipopolysaccharide biosynthesis protein wbpB | ||||||
Keywords | OXIDOREDUCTASE / sugar biosynthesis / dehydrogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.449 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 | 3o9z.cif.gz | 284.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o9z.ent.gz | 230.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/3o9z ftp://data.pdbj.org/pub/pdb/validation_reports/o9/3o9z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34831.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C0287, wbpB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q72KX8 |
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-Non-polymers , 5 types, 1231 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-AKG / #4: Chemical | ChemComp-CL / #5: Chemical | #6: 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: 2.87 Å3/Da / Density % sol: 57.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15-20% PEG-5000, 100 mM MOPS, 20 mM alpha-ketoglutarate, pH 7, 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: 0.97918,0.97953,0.97150 | ||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 14, 2009 / Details: mirrors | ||||||||||||
Radiation | Monochromator: double crystal Si-111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.449→50 Å / Num. all: 270515 / Num. obs: 270515 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 44.4 | ||||||||||||
Reflection shell | Resolution: 1.449→1.48 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 4.2 / Num. unique all: 12317 / Rsym value: 0.167 / % possible all: 88.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.449→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.141 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.016 Å2
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Refinement step | Cycle: LAST / Resolution: 1.449→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.449→1.487 Å / Total num. of bins used: 20
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