+Open data
-Basic information
Entry | Database: PDB / ID: 3wby | ||||||
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Title | Crystal structure of Gox0644 D53A mutant in complex with NADPH | ||||||
Components | Putative 2,5-diketo-D-gluconic acid reductase | ||||||
Keywords | OXIDOREDUCTASE / Aldo-keto reductase (AKR) / reductase / NADPH | ||||||
Function / homology | Function and homology information 2,5-didehydrogluconate reductase activity / small molecule metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / nucleotide binding Similarity search - Function | ||||||
Biological species | Gluconobacter oxydans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Yuan, Y.A. / Wang, C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Gox0644 D53A mutant in complex with NADPH Authors: Yuan, Y.A. / Wang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wby.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wby.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/3wby ftp://data.pdbj.org/pub/pdb/validation_reports/wb/3wby | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32009.264 Da / Num. of mol.: 2 / Mutation: D53A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: 621H / Gene: GOX0644 / Production host: Escherichia coli (E. coli) References: UniProt: Q5FT75, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor #2: Chemical | |
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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: 2.09 Å3/Da / Density % sol: 41.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG3350, Li2SO4, Bis-tris, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011 |
Radiation | Monochromator: 180 degree collection, 1 degree oscillation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0075 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 9300 / Num. obs: 9300 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % |
Reflection shell | Resolution: 3.2→3.26 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.57 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.83 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 38.92 / SU ML: 0.675 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.755 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.19 Å2 / Biso mean: 60.0367 Å2 / Biso min: 25.68 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→48.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.205→3.288 Å / Total num. of bins used: 20
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