+Open data
-Basic information
Entry | Database: PDB / ID: 2xj5 | ||||||
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Title | The structure of cytochrome c peroxidase Compound II | ||||||
Components | CYTOCHROME C PEROXIDASE, MITOCHONDRIAL | ||||||
Keywords | OXIDOREDUCTASE / ASCORBATE PEROXIDASE / FERRYL ION / FERROUS HEME | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / 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: 1.69 Å | ||||||
Authors | Gumiero, A. / Raven, E.L. / Moody, P.C.E. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2011 Title: Nature of the ferryl heme in compounds I and II. Authors: Gumiero, A. / Metcalfe, C.L. / Pearson, A.R. / Raven, E.L. / Moody, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xj5.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xj5.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/2xj5 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/2xj5 | HTTPS FTP |
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-Related structure data
Related structure data | 2xi6C 2xifC 2xihC 2xilC 2xj6C 2xj8C 2v2eS 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: 33633.398 Da / Num. of mol.: 1 / Fragment: RESIDUES 71-361 Source method: isolated from a genetically manipulated source Details: COMPOUND I Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Organ: MITOCHONDRION MATRIX / Plasmid: PLEICS03 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: P00431, cytochrome-c peroxidase | ||||||
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#2: Chemical | ChemComp-HEM / | ||||||
#3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Sequence details | (CCPR_YEAST) | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.65 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: KPI 50 MM PH 6.5, MPD 30% VOLUME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→1.76 Å / Num. obs: 39037 / % possible obs: 83.5 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.4 / % possible all: 75.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V2E Resolution: 1.69→33.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.093 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.625 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→33.14 Å
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Refine LS restraints |
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