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Yorodumi- PDB-4bjz: Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lip... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bjz | ||||||
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Title | Crystal structure of 3-hydroxybenzoate 6-hydroxylase uncovers lipid- assisted flavoprotein strategy for regioselective aromatic hydroxylation: Native data | ||||||
Components | PROBABLE SALICYLATE MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / GENTISATE / 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: 1.51 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 | 4bjz.cif.gz | 179.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bjz.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/4bjz ftp://data.pdbj.org/pub/pdb/validation_reports/bj/4bjz | HTTPS FTP |
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-Related structure data
Related structure data | 4bjySC 4bk1C 4bk2C 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: 46948.242 Da / Num. of mol.: 1 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: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 28% PEG 4000, 0.2 M SODIUM ACETATE 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→33.7 Å / Num. obs: 63875 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.51→1.54 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.5 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BJY Resolution: 1.51→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.131 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.076 / 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: 19.992 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→30 Å
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Refine LS restraints |
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