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- PDB-1ebe: Laue diffraction study on the structure of cytochrome c peroxidas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ebe | ||||||
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Title | Laue diffraction study on the structure of cytochrome c peroxidase compound I | ||||||
![]() | CYTOCHROME C PEROXIDASE | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (H2O2(A)) / COMPOUND I / LAUE DIFFRACTION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Fulop, V. / Phizackerley, R.P. / Soltis, S.M. / Clifton, I.J. / Wakatsuki, S. / Erman, J.E. / Hajdu, J. / Edwards, S.L. | ||||||
![]() | ![]() Title: Laue Diffraction Study on the Structure of Cytochrome C Peroxidase Compound I Authors: Fulop, V. / Phizackerley, R.P. / Soltis, S.M. / Clifton, I.J. / Wakatsuki, S. / Erman, J.E. / Hajdu, J. / Edwards, S.L. #1: ![]() Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7 Angstroms Resolution Authors: Finzel, B.C. / Poulos, T.L. / Kraut, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.9 KB | Display | ![]() |
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PDB format | ![]() | 60.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
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Full document | ![]() | 487.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cypS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 33572.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPOUND I / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-O / |
#4: Water | ChemComp-HOH / |
Compound details | REMOVES TOXIC RADICALS THAT ARE PRODUCED WITHIN CELLS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.04 % |
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Crystal grow | pH: 6 Details: SEE REFERENCE EDWARDS ET AL. BIOCHEMISTRY 26, 1503-1511 (1987), pH 6.00 |
Crystal grow | *PLUS Method: other / Details: Edwards, S.L., (1987) Biochemistry, 26, 1503. |
-Data collection
Diffraction | Mean temperature: 279 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() ![]() ![]() | |||||||||
Detector | Type: KODAK DEF5 / Detector: FILM / Date: Nov 15, 1990 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→8 Å / Num. obs: 9089 / % possible obs: 42 % / Observed criterion σ(I): -2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 37.5 | |||||||||
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 30274 / Num. measured all: 94847 / Rmerge(I) obs: 0.08 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2CYP Resolution: 2.2→8 Å / σ(F): 2 Details: OMITTED FROM THIS ENTRY ARE DISORDERED SURFACE ATOMS WHOSE POSITION COULD NOT BE DETERMINED EVEN AFTER REFINEMENT. ALL ATOMS PRESENT IN ENTRY 2CYP WERE USED IN REFINEMENT
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Displacement parameters | Biso mean: 32.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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