+Open data
-Basic information
Entry | Database: PDB / ID: 1z53 | ||||||
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Title | The 1.13 Angstrom Structure of Iron-free Cytochrome c Peroxidase | ||||||
Components | Cytochrome c peroxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / CcP / Heme peroxidase / Iron-free protoporphyrin IX / Trp cation radical | ||||||
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 / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.13 Å | ||||||
Authors | Bhaskar, B. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2005 Title: The 1.13-A structure of iron-free cytochrome c peroxidase. Authors: Bhaskar, B. / 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 | 1z53.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z53.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 1z53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/1z53 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/1z53 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 33571.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Tissue fraction: Protein present in yeast inner mitochondrial membrane Gene: CCP1, CCP, CPO / Plasmid: Poulos Vector (modified pT7) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / Keywords: Cytochrome c Peroxidase / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-PP9 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 30% 2-methyl-2,4-pentanediol (MPD), 50 mM Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 116 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 / Wavelength: 0.78 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 18, 2003 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.78 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→100 Å / Num. all: 189599 / Num. obs: 189599 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.625 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.13→1.16 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.55 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: Atomic resolution structure of Wild Type CcP Resolution: 1.13→10 Å / Num. parameters: 23795 / Num. restraintsaints: 28345 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 16 / Occupancy sum hydrogen: 2223.1 / Occupancy sum non hydrogen: 2935.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→10 Å
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Refine LS restraints |
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