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Yorodumi- PDB-1zby: High-Resolution Crystal Structure of Native (Resting) Cytochrome ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zby | ||||||
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Title | High-Resolution Crystal Structure of Native (Resting) Cytochrome c Peroxidase (CcP) | ||||||
Components | Cytochrome c peroxidase | ||||||
Keywords | OXIDOREDUCTASE / CcP / Heme Peroxidase / Resting State / Trp-cation radical / High-spin heme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Bonagura, C.A. / Bhaskar, B. / Shimizu, H. / Li, H. / Sundaramoorthy, M. / McRee, D.E. / Goodin, D.B. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: High-resolution crystal structures and spectroscopy of native and compound I cytochrome c peroxidase Authors: Bonagura, C.A. / Bhaskar, B. / Shimizu, H. / Li, H. / Sundaramoorthy, M. / McRee, D.E. / Goodin, D.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 | 1zby.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zby.ent.gz | 136 KB | Display | PDB format |
PDBx/mmJSON format | 1zby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zby ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zby | HTTPS FTP |
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-Related structure data
Related structure data | 1zbzC 2cypS 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: 33571.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: Modified pT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#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), 50mM Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1999 / 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: 1.2→100 Å / Num. all: 1275193 / Num. obs: 126775 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.05 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.2→1.22 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.99 / % possible all: 74 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2CYP Resolution: 1.2→100 Å / Num. parameters: 29580 / Num. restraintsaints: 34311 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 18 / Occupancy sum hydrogen: 2222 / Occupancy sum non hydrogen: 3123 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→100 Å
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Refine LS restraints |
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