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- PDB-7bby: Crystal structure of aldo-keto reductase with C-terminal His tag ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bby | ||||||
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Title | Crystal structure of aldo-keto reductase with C-terminal His tag from Agrobacterium tumefaciens | ||||||
![]() | Aryl-alcohol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Aldo-keto reductase / histidine / sulfoquinovose | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Snow, A. / Sharma, M. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.4 KB | Display | ![]() |
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Full document | ![]() | 428 KB | Display | |
Data in XML | ![]() | 13.7 KB | Display | |
Data in CIF | ![]() | 19.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bbzC ![]() 7bc0C ![]() 7bc1C ![]() 7nbzC ![]() 7ofxC ![]() 7ofyC ![]() 7oh2C ![]() 7olfC ![]() 4r9oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33019.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: C58 / ATCC 33970 / Gene: Atu3278 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.056 M sodium phosphate monobasic/monohydrate 1.344 M potassium phosphate dibasic protein at 20mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→44.51 Å / Num. obs: 38236 / % possible obs: 100 % / Redundancy: 24.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.039 / Rrim(I) all: 0.193 / Net I/σ(I): 14.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4r9o Resolution: 1.83→44.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.75 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.1 / 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: 82.59 Å2 / Biso mean: 31.964 Å2 / Biso min: 20.88 Å2
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Refinement step | Cycle: final / Resolution: 1.83→44.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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