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- PDB-1kxn: Crystal Structure of Cytochrome c Peroxidase with a Proposed Elec... -
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Open data
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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. | ||||||
![]() | cytochrome c peroxidase | ||||||
![]() | OXIDOREDUCTASE / engineered heme channel | ||||||
Function / homology | ![]() cytochrome-c peroxidase / cytochrome-c peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rosenfeld, R.J. / Hayes, A.M.A. / Musah, R.A. / Goodin, D.B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82 KB | Display | ![]() |
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PDB format | ![]() | 59.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.6 KB | Display | ![]() |
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Full document | ![]() | 477.4 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kxmC ![]() 1cmqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: CCP-MKT / Plasmid: PT7CCP / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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