+Open data
-Basic information
Entry | Database: PDB / ID: 4cy8 | ||||||
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Title | 2-hydroxybiphenyl 3-monooxygenase (HbpA) in complex with FAD | ||||||
Components | 2-HYDROXYBIPHENYL 3-MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / BIOTRANSFORMATIONS / HYDROXYLATION / FLAVIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS NITROREDUCENS HBP1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Jensen, C.N. / Farrugia, J.E. / Frank, A. / Man, H. / Hart, S. / Turkenburg, J.P. / Grogan, G. | ||||||
Citation | Journal: Chembiochem / Year: 2015 Title: Structures of the Apo and Fad-Bound Forms of 2-Hydroxybiphenyl 3-Monooxygenase (Hbpa) Locate Activity Hotspots Identified by Using Directed Evolution. Authors: Jensen, C.N. / Mielke, T. / Farrugia, J.E. / Frank, A. / Man, H. / Hart, S. / Turkenburg, J.P. / Grogan, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cy8.cif.gz | 445.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cy8.ent.gz | 358.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cy8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/4cy8 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/4cy8 | HTTPS FTP |
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-Related structure data
Related structure data | 4cy6C 3ihgS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 63863.367 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS NITROREDUCENS HBP1 (bacteria) Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06647, EC: 1.14.13.44 #2: Chemical | ChemComp-FDA / #3: Water | ChemComp-HOH / | Sequence details | MUTATION T347Q IS PRESENT | |
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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: 2.71 Å3/Da / Density % sol: 54.7 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 18% (W/V) PEG 3350, 0.15 M KSCN, 1 MM FAD IN BIS-TRIS PROPANE BUFFER AT PH 5.5, WITH A PROTEIN CONCENTRATION OF 10 MG ML-1 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91999 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91999 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→59.53 Å / Num. obs: 146673 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IHG Resolution: 2.03→59.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.133 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.154 / 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: 35.258 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→59.53 Å
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Refine LS restraints |
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