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Yorodumi- PDB-4bk2: Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bk2 | ||||||
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Title | Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid- assisted flavoprotein strategy for regioselective aromatic hydroxylation: Q301E mutant | ||||||
Components | PROBABLE SALICYLATE MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / GENTISATE / HYDROXYLASE / MONOOXYGENASE / PHOSPHOLIPID | ||||||
Function / homology | Function and homology information salicylate 1-monooxygenase / salicylate 1-monooxygenase activity / FAD binding Similarity search - Function | ||||||
Biological species | RHODOCOCCUS JOSTII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å | ||||||
Authors | Orru, R. / Montersino, S. / Barendregt, A. / Westphal, A.H. / van Duijn, E. / Mattevi, A. / van Berkel, W.J.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal Structure of 3-Hydroxybenzoate 6-Hydroxylase Uncovers Lipid-Assisted Flavoprotein Strategy for Regioselective Aromatic Hydroxylation Authors: Montersino, S. / Orru, R. / Barendregt, A. / Westphal, A.H. / Van Duijn, E. / Mattevi, A. / Van Berkel, W.J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bk2.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bk2.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bk2 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bk2 | HTTPS FTP |
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-Related structure data
Related structure data | 4bjySC 4bjzC 4bk1C 4bk3C S: Starting model for refinement C: citing same article (ref.) |
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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: 46949.227 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOCOCCUS JOSTII (bacteria) / Strain: RHA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 References: UniProt: Q0SFK6, salicylate 1-monooxygenase, EC: 1.14.13.24 |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-P3A / |
#4: Water | ChemComp-HOH / |
Sequence details | PRESENCE OF 6XHIS TAG AT C-TERM |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.17 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 30% PEG 4000, 0.2 M LISO4 AND 0.1 M TRIS/HCL (PH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→71.39 Å / Num. obs: 15081 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.47→2.57 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BJY Resolution: 2.47→85.38 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.89 / SU B: 15.256 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.676 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 197-198 ARE DISORDERED
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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: 21.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.47→85.38 Å
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Refine LS restraints |
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