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Yorodumi- PDB-3m2h: Crystallographic and Single Crystal Spectral Analysis of the Pero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m2h | ||||||
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Title | Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate | ||||||
Components | Cytochrome c peroxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome c peroxidase (CCP) / Heme / Hydrogen peroxide / Iron / Metal-binding / Mitochondrion / Peroxidase | ||||||
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 / SYNCHROTRON / AB INITIO / Resolution: 1.4 Å | ||||||
Authors | Meharenna, Y.T. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate. Authors: Meharenna, Y.T. / Doukov, T. / Li, H. / Soltis, S.M. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m2h.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m2h.ent.gz | 127 KB | Display | PDB format |
PDBx/mmJSON format | 3m2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m2h_validation.pdf.gz | 755.9 KB | Display | wwPDB validaton report |
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Full document | 3m2h_full_validation.pdf.gz | 759.3 KB | Display | |
Data in XML | 3m2h_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3m2h_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/3m2h ftp://data.pdbj.org/pub/pdb/validation_reports/m2/3m2h | HTTPS FTP |
-Related structure data
Related structure data | 3m23C 3m25C 3m26C 3m27C 3m28C 3m29C 3m2aC 3m2bC 3m2cC 3m2dC 3m2eC 3m2fC 3m2gC 3m2iC 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: 33315.012 Da / Num. of mol.: 1 / Fragment: UNP residues 71-361 / Mutation: N184R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP, CCP1, CPO, YKR066C / 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 | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 19 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 60.19 % |
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Crystal grow | Temperature: 277.2 K / pH: 6 Details: 10uL (350-400uM protein), 22% MPD, 50mM tris phoshate buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K |
-Data collection
Diffraction | Mean temperature: 65 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.954 |
Detector | Detector: CCD / Date: Nov 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 82025 / % possible obs: 100 % / Redundancy: 29 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 28.3 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 12.3 / Rsym value: 0.388 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.4→50 Å / Num. parameters: 36595 / Num. restraintsaints: 33062 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 2206.99 / Occupancy sum non hydrogen: 2964 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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Refine LS restraints |
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