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Yorodumi- PDB-1mk8: Crystal Structure of a Mutant Cytochrome c Peroxidase showing a N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mk8 | ||||||
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Title | Crystal Structure of a Mutant Cytochrome c Peroxidase showing a Novel Trp-Tyr Covalent Cross-link | ||||||
Components | Cytochrome c Peroxidase | ||||||
Keywords | OXIDOREDUCTASE / cytochrome c peroxidase / oxygen radical / Tryptophan-Tyrosine cross-link / Trp cation radical | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Bhaskar, B. / Immoos, C.E. / Shimizu, H. / Farmer, P.J. / Poulos, T.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: A Novel Heme and Peroxide-Dependent Tryptophan-Tyrosine Cross-Link in a Mutant of Cytochrome c Peroxidase Authors: Bhaskar, B. / Immoos, C.E. / Shimizu, H. / Sulc, F. / Farmer, P.J. / Poulos, T.L. | ||||||
History |
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Remark 400 | COMPOUND HELICAL BUNDLE PROTEIN WITH A DISTINCT DISTAL AND PROXIMAL HEME DOMAINS. PROXIMAL HEME ...COMPOUND HELICAL BUNDLE PROTEIN WITH A DISTINCT DISTAL AND PROXIMAL HEME DOMAINS. PROXIMAL HEME DOMAIN CONTAINS TRP191 WHICH FORMS A CATIONIC RADICAL DURING ELECTRON TRANSFER WITH ITS REDOX PARTNER CYTOCHROME C. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mk8.cif.gz | 88 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mk8.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mk8_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
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Full document | 1mk8_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 1mk8_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1mk8_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/1mk8 ftp://data.pdbj.org/pub/pdb/validation_reports/mk/1mk8 | HTTPS FTP |
-Related 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: 33596.266 Da / Num. of mol.: 1 / Mutation: H52Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: OPBYC / Plasmid: pT7CcP / 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: 3.06 Å3/Da / Density % sol: 59.82 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 2-Methyl-2,4-Pentanediol (MPD), tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 116 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 6, 2000 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 50278 / % possible obs: 11.56 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.645 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.63 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.275 / Num. unique all: 2419 / % possible all: 0.0055 |
Reflection | *PLUS Lowest resolution: 100 Å / % possible obs: 99.4 % / Num. measured all: 434660 |
Reflection shell | *PLUS % possible obs: 98.2 % / Rmerge(I) obs: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ultrahigh resolution structure of WTCcP Resolution: 1.65→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement | *PLUS % reflection Rfree: 4.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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