[English] 日本語

- PDB-1kxm: Crystal structure of Cytochrome c Peroxidase with a Proposed Elec... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kxm | ||||||
---|---|---|---|---|---|---|---|
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 / peroxidase activity / mitochondrial intermembrane space / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 82.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 60.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 495.4 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kxnC ![]() 1cmqS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33029.688 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: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-BZI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.01 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.74→10 Å / Num. all: 33260 / Num. obs: 33260 / % possible obs: 77.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.046 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.74→1.8 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2794 / % possible all: 40.1 |
Reflection | *PLUS % possible obs: 77.8 % / Num. measured all: 105851 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS Lowest resolution: 1.8 Å / % possible obs: 40.1 % / Num. unique obs: 2794 / Num. measured obs: 4827 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CMQ Resolution: 1.74→10 Å / Num. parameters: 11043 / Num. restraintsaints: 9782 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2760 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor all: 0.1937 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|