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Open data
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Basic information
Entry | Database: PDB / ID: 2xj5 | ||||||
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Title | The structure of cytochrome c peroxidase Compound II | ||||||
![]() | CYTOCHROME C PEROXIDASE, MITOCHONDRIAL | ||||||
![]() | OXIDOREDUCTASE / ASCORBATE PEROXIDASE / FERRYL ION / FERROUS HEME | ||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gumiero, A. / Raven, E.L. / Moody, P.C.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.2 KB | Display | ![]() |
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PDB format | ![]() | 71.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.3 KB | Display | ![]() |
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Full document | ![]() | 840.4 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xi6C ![]() 2xifC ![]() 2xihC ![]() 2xilC ![]() 2xj6C ![]() 2xj8C ![]() 2v2eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Organ: MITOCHONDRION MATRIX / Plasmid: PLEICS03 / Production host: ![]() ![]() | ||||||
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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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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