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Yorodumi- PDB-4z6v: Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z6v | |||||||||
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Title | Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-nitrocatechol at 1.37 Ang resolution | |||||||||
Components | Homoprotocatechuate 2,3-dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE / Dioxygenase / 2-His-1-carboxylate facial triad / oxygen activation / acid-base catalysis | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Brevibacterium fuscum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | |||||||||
Authors | Kovaleva, E.G. / Lipscomb, J.D. | |||||||||
Funding support | United Kingdom, United States, 2items
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Citation | Journal: Biochemistry / Year: 2015 Title: Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Authors: Kovaleva, E.G. / Rogers, M.S. / Lipscomb, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z6v.cif.gz | 667.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z6v.ent.gz | 549.3 KB | Display | PDB format |
PDBx/mmJSON format | 4z6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/4z6v ftp://data.pdbj.org/pub/pdb/validation_reports/z6/4z6v | HTTPS FTP |
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-Related structure data
Related structure data | 4z6lC 4z6mC 4z6nC 4z6oC 4z6pC 4z6qC 4z6rC 4z6sC 4z6tC 4z6uC 4z6wC 4z6zC 3ojtS 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41745.305 Da / Num. of mol.: 4 / Mutation: H200Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Plasmid: pYZW204 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: Q45135 |
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-Non-polymers , 6 types, 1954 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-P6G / #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-4NC / | #7: 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: 2.39 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 14% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCL |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 6, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.37→45.691 Å / Num. all: 325847 / Num. obs: 325847 / % possible obs: 97.9 % / Redundancy: 4.1 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.073 / Rsym value: 0.064 / Net I/av σ(I): 10.779 / Net I/σ(I): 14.2 / Num. measured all: 1340516 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OJT Resolution: 1.37→40.35 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.1415 / WRfactor Rwork: 0.1067 / FOM work R set: 0.9016 / SU B: 2.023 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0455 / SU Rfree: 0.0465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.5 Å2 / Biso mean: 16.321 Å2 / Biso min: 6.65 Å2
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Refinement step | Cycle: final / Resolution: 1.37→40.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Total num. of bins used: 20
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