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Yorodumi- PDB-1ebe: Laue diffraction study on the structure of cytochrome c peroxidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ebe | ||||||
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Title | Laue diffraction study on the structure of cytochrome c peroxidase compound I | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / OXIDOREDUCTASE (H2O2(A)) / COMPOUND I / LAUE DIFFRACTION | ||||||
Function / homology | Function and homology information 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 | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Fulop, V. / Phizackerley, R.P. / Soltis, S.M. / Clifton, I.J. / Wakatsuki, S. / Erman, J.E. / Hajdu, J. / Edwards, S.L. | ||||||
Citation | Journal: Structure / Year: 1994 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: Journal: J.Biol.Chem. / Year: 1984 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ebe.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ebe.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ebe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1ebe ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1ebe | HTTPS FTP |
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-Related structure data
Related structure data | 2cypS S: Starting model for refinement |
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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: 33572.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: COMPOUND I / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00431, cytochrome-c peroxidase |
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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: X-RAY DIFFRACTION / Number of used crystals: 4 |
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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: SYNCHROTRON / Site: CHESS / Type: CHESS / Wavelength: 0.2-2.5 | |||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS 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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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