[English] 日本語
![](img/lk-miru.gif)
- PDB-1dcc: 2.2 ANGSTROM STRUCTURE OF OXYPEROXIDASE: A MODEL FOR THE ENZYME:P... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1dcc | ||||||
---|---|---|---|---|---|---|---|
Title | 2.2 ANGSTROM STRUCTURE OF OXYPEROXIDASE: A MODEL FOR THE ENZYME:PEROXIDE COMPLEX | ||||||
![]() | CYTOCHROME C PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE(H2O2(A)) | ||||||
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 | ![]() | ||||||
![]() | Miller, M.A. / Shaw, A. / Kraut, J. | ||||||
![]() | ![]() Title: 2.2 A structure of oxy-peroxidase as a model for the transient enzyme: peroxide complex. Authors: Miller, M.A. / Shaw, A. / Kraut, J. #1: ![]() Title: Reaction of Ferrous Cytochrome C Peroxidase with Dioxygen: Site-Directed Mutagenesis Provides Evidence for Rapid Reduction of Dioxygen by Intramolecular Electron Transfer from the Compound I Radical Site Authors: Miller, M.A. / Bandyopadhyay, D. / Mauro, J.M. / Taylor, T.G. / Kraut, J. #2: ![]() Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme Cleft Mutants Prepared by Site-Directed Mutagenesis Authors: Wang, J. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J. #3: ![]() Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7 Angstroms Resolution Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33730.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00431, cytochrome-c peroxidase |
---|---|
#2: Chemical | ChemComp-OXY / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE DIFFERS FROM THAT REPORTED FOR 2CYP AT RESIDUE 272. IN THE PRESENT ENTRY, THIS RESIDUE ...THE SEQUENCE DIFFERS FROM THAT REPORTED FOR 2CYP AT RESIDUE 272. IN THE PRESENT ENTRY, THIS RESIDUE IS REPORTED AS ASN. THIS CORRECTS AN ERROR INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, sitting drop / Details: referred to Biochemistry 29.7160-7173 1990 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / % possible obs: 87 % / Num. measured all: 16002 |
-
Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Highest resolution: 2.2 Å /
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.155 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|