+Open data
-Basic information
Entry | Database: PDB / ID: 4a6z | ||||||
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Title | Cytochrome c peroxidase with bound guaiacol | ||||||
Components | CYTOCHROME C PEROXIDASE, MITOCHONDRIAL | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Murphy, E.J. / Metcalfe, C.L. / Nnamchi, C. / Raven, E.L. / Moody, P.C.E. | ||||||
Citation | Journal: FEBS J. / Year: 2012 Title: Crystal Structure of Guaiacol and Phenol Bound to a Heme Peroxidase. Authors: Murphy, E.J. / Metcalfe, C.L. / Nnamchi, C. / Moody, P.C.E. / Raven, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a6z.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a6z.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 4a6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/4a6z ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a6z | HTTPS FTP |
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-Related structure data
Related structure data | 4a71C 4a78C 4a7mC 2v23S 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
#1: Protein | Mass: 33781.621 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PT7CCP/Y39A/N184R / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.43 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC R-AXIS 4 / Detector: IMAGE PLATE / Date: Oct 15, 2006 / Details: MULTILAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→27.2 Å / Num. obs: 46241 / % possible obs: 85.1 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.61→1.69 Å / Redundancy: 1.35 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.6 / % possible all: 25.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V23 Resolution: 1.61→27.24 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.311 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.091 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.973 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→27.24 Å
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Refine LS restraints |
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