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Yorodumi- PDB-4z2u: Crystal Structure of 2-hydroxybiphenyl 3-monooxygenase R242Q from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z2u | |||||||||
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Title | Crystal Structure of 2-hydroxybiphenyl 3-monooxygenase R242Q from Pseudomonas azelaica | |||||||||
Components | 2-hydroxybiphenyl-3-monooxygenase | |||||||||
Keywords | OXIDOREDUCTASE / flavin dependent oxygenase | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding Similarity search - Function | |||||||||
Biological species | Pseudomonas nitroreducens HBP1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | |||||||||
Authors | Kanteev, M. / Bregman-Cohen, A. / Fishman, A. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2015 Title: A crystal structure of 2-hydroxybiphenyl 3-monooxygenase with bound substrate provides insights into the enzymatic mechanism. Authors: Kanteev, M. / Bregman-Cohen, A. / Deri, B. / Shahar, A. / Adir, N. / Fishman, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z2u.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z2u.ent.gz | 191.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z2u_validation.pdf.gz | 1013 KB | Display | wwPDB validaton report |
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Full document | 4z2u_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4z2u_validation.xml.gz | 50.5 KB | Display | |
Data in CIF | 4z2u_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z2u ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z2u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 64636.156 Da / Num. of mol.: 2 / Mutation: R242Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas nitroreducens HBP1 (bacteria) Gene: hbpA / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / References: UniProt: O06647, EC: 1.14.13.44 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium citrate and 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.56 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.56 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.14 Å / Num. obs: 49676 / % possible obs: 92.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.7 |
Reflection shell | Rmerge(I) obs: 0.191 |
-Processing
Software |
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Refinement | Resolution: 2.5→32.373 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.404 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→32.373 Å
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Refine LS restraints |
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LS refinement shell |
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