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Yorodumi- PDB-1kxn: Crystal Structure of Cytochrome c Peroxidase with a Proposed Elec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kxn | ||||||
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Title | Crystal Structure of Cytochrome c Peroxidase with a Proposed Electron Transfer Pathway Excised to Form a Ligand Binding Channel. | ||||||
Components | cytochrome c peroxidase | ||||||
Keywords | OXIDOREDUCTASE / engineered heme channel | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Rosenfeld, R.J. / Hayes, A.M.A. / Musah, R.A. / Goodin, D.B. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel. Authors: Rosenfeld, R.J. / Hays, A.M. / Musah, R.A. / Goodin, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kxn.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kxn.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/1kxn ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kxn | HTTPS FTP |
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-Related structure data
Related structure data | 1kxmC 1cmqS 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: 32928.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-362, NUMBERED 4-292 / Mutation: P190G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP-MKT / 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: 3.14 Å3/Da / Density % sol: 60.82 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1996 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 35095 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.075 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.5 % / Num. unique all: 3208 / % possible all: 81.1 |
Reflection | *PLUS Num. obs: 36741 / Num. measured all: 168657 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 81.1 % / Num. unique obs: 3208 / Num. measured obs: 11517 / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CMQ Resolution: 1.8→10 Å / Num. parameters: 10827 / Num. restraintsaints: 9732 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2706 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor all: 0.1871 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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