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- PDB-3zv6: CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zv6 | ||||||
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Title | CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT ANALOG 4,4'-DIHYDROXYBIPHENYL | ||||||
![]() | CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE/OXIDOREDUCTASE / SDR | ||||||
Function / homology | ![]() cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity / carbonyl reductase (NADPH) activity / : Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dhindwal, S. / Patil, D.N. / Kumar, P. | ||||||
![]() | ![]() Title: Biochemical Studies and Ligand-Bound Structures of Biphenyl Dehydrogenase from Pandoraea Pnomenusa Strain B-356 Reveal a Basis for Broad Specificity of the Enzyme. Authors: Dhindwal, S. / Patil, D.N. / Mohammadi, M. / Sylvestre, M. / Tomar, S. / Kumar, P. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Expression, Purification, Crystallization and Preliminary Crystallographic Studies of Cis-Biphenyl-2,3-Dihydrodiol-2,3-Dehydrogenase from Pandoraea Pnomenusa B-356. Authors: Patil, D.N. / Tomar, S. / Sylvestre, M. / Kumar, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216 KB | Display | ![]() |
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PDB format | ![]() | 174.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y93C ![]() 2y99C ![]() 3zv3C ![]() 3zv4C ![]() 3zv5C ![]() 1bdbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29381.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q46381, cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase #2: Chemical | #3: Chemical | ChemComp-4HB / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.63 % / Description: NONE |
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Crystal grow | Details: SODIUM MALONATE, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2011 |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97841 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→100 Å / Num. obs: 30090 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 38.421 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.34 |
Reflection shell | Resolution: 2.15→70.19 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.51 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BDB Resolution: 2.14→70.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.885 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 40.406 Å2
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Refinement step | Cycle: LAST / Resolution: 2.14→70.19 Å
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Refine LS restraints |
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