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Yorodumi- PDB-7bc1: Crystal structure of aldo-keto reductase from Agrobacterium tumef... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bc1 | ||||||
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Title | Crystal structure of aldo-keto reductase from Agrobacterium tumefaciens in a ternary complex with NADPH and glucose | ||||||
Components | Aryl-alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Aldo-keto reductase / NADPH / glucose / sulfoquinovose | ||||||
Function / homology | Function and homology information 6-dehydroglucose reductase / carbohydrate metabolic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Agrobacterium fabrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Snow, A. / Sharma, M. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / ...Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / Ascher, D.B. / McConville, M.J. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bc1.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bc1.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 7bc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/7bc1 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/7bc1 | HTTPS FTP |
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-Related structure data
Related structure data | 7bbySC 7bbzC 7bc0C 7nbzC 7ofxC 7ofyC 7oh2C 7olfC 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: 34326.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: Atu3278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CEY6 |
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#2: Chemical | ChemComp-NAP / |
#3: Sugar | ChemComp-GLC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2328458 Å3/Da / Density % sol: 44.947571 % / Description: Hexagonal plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M SPG 25% PEG 1500 In-drop protein concentration of 13 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→52.57 Å / Num. obs: 48238 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Net I/σ(I): 14.7 / Num. measured all: 571667 / Scaling rejects: 68 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BBY Resolution: 1.5→52.51 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.001 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.069 / 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: 57.16 Å2 / Biso mean: 21.006 Å2 / Biso min: 13.7 Å2
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Refinement step | Cycle: final / Resolution: 1.5→52.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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