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Yorodumi- PDB-3uce: Crystal structure of a small-chain dehydrogenase in complex with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uce | ||||||
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Title | Crystal structure of a small-chain dehydrogenase in complex with NADPH | ||||||
Components | Dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / Small-chain dehydrogenase | ||||||
Function / homology | Function and homology information oxidoreductase activity / nucleotide binding / identical protein binding Similarity search - Function | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Buysschaert, G. / Verstraete, K. / Savvides, S. / Vergauwen, B. | ||||||
Citation | Journal: Febs J. / Year: 2013 Title: Structural and biochemical characterization of an atypical short-chain dehydrogenase/reductase reveals an unusual cofactor preference. Authors: Buysschaert, G. / Verstraete, K. / Savvides, S.N. / Vergauwen, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uce.cif.gz | 335.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uce.ent.gz | 277.1 KB | Display | PDB format |
PDBx/mmJSON format | 3uce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/3uce ftp://data.pdbj.org/pub/pdb/validation_reports/uc/3uce | HTTPS FTP |
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-Related structure data
Related structure data | 3ucfC 1o5iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 23680.973 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: VVA1599 / Plasmid: pACYCDuet-I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MBY8 #2: Chemical | ChemComp-NDP / #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: 2.48 Å3/Da / Density % sol: 50.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5, 18% PEG-5000, Protein concentration: 8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99993 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2011 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99993 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→40 Å / Num. all: 85740 / Num. obs: 84971 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.78 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.54 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.41 / Num. unique all: 13760 / % possible all: 97 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1O5I Resolution: 1.798→39.201 Å / SU ML: 0.46 / Isotropic thermal model: isotropic - one B-factor per atom / σ(F): 1.99 / Phase error: 21.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.281 Å2 / ksol: 0.401 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.798→39.201 Å
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Refine LS restraints |
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LS refinement shell |
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