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Yorodumi- PDB-3zv3: CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zv3 | ||||||
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Title | CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B-356 IN INTERMEDIATE STATE OF SUBSTRATE BINDING LOOP | ||||||
Components | CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE/OXIDOREDUCTASE / SDR / COMAMONAS TESTOSTERONI | ||||||
Function / homology | Function and homology information 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 | PANDORAEA PNOMENUSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Dhindwal, S. / Patil, D.N. / Kumar, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zv3.cif.gz | 97 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zv3.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 3zv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zv3_validation.pdf.gz | 437 KB | Display | wwPDB validaton report |
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Full document | 3zv3_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 3zv3_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 3zv3_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/3zv3 ftp://data.pdbj.org/pub/pdb/validation_reports/zv/3zv3 | HTTPS FTP |
-Related structure data
Related structure data | 2y93C 2y99C 3zv4C 3zv5C 3zv6C 1bdbS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) PANDORAEA PNOMENUSA (bacteria) / Strain: B-356 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q46381, cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase #2: 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: 2.21 Å3/Da / Density % sol: 44.43 % / 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: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2010 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 13445 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 70.134 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.44 |
Reflection shell | Resolution: 2.9→69.67 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.08 / % possible all: 98.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BDB Resolution: 2.9→69.67 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.864 / SU B: 23.302 / SU ML: 0.427 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / 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: 49.376 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→69.67 Å
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