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Yorodumi- PDB-1bem: INTERACTION BETWEEN PROXIMAL AND DISTALS REGIONS OF CYTOCHROME C ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bem | ||||||
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Title | INTERACTION BETWEEN PROXIMAL AND DISTALS REGIONS OF CYTOCHROME C PEROXIDASE | ||||||
Components | CYTOCHROME C PEROXIDASE | ||||||
Keywords | PEROXIDASE / OXIDOREDUCTASE | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Kraut, M.A.M.J. | ||||||
Citation | Journal: To be Published Title: Interaction between Proximal and Distals Regions of Cytochrome C Peroxidase Authors: Miller, M.A. / Han, G.W. / Kraut, J. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: A Ligand-Gated, Hinged Loop Rearrangement Opens a Channel to a Buried Artificial Protein Cavity Authors: Fitzgerald, M.M. / Musah, R.A. / Mcree, D.E. / Goodin, D.B. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: A Cation Binding Motif Stabilizes the Compound I Radical of Cytochrome C Peroxidase Authors: Miller, M.A. / Han, G.W. / Kraut, J. #3: Journal: Biochemistry / Year: 1990 Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme-Cleft Mutants Prepared by Site-Directed Mutagenesis Authors: Wang, J.M. / Mauro, M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.H. / Kraut, J. #4: Journal: Biochemistry / Year: 1987 Title: Yeast Cytochrome C Peroxidase: Mutagenesis and Expression in Escherichia Coli Show Tryptophan-51 is not the Radical Site in Compound I Authors: Fishel, L.A. / Villafranca, J.E. / Mauro, J.M. / Kraut, J. #5: Journal: J.Biol.Chem. / Year: 1984 Title: Crystal Structure of Yeast Cytochrome C Peroxidase Refined at 1.7-A 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 | 1bem.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bem.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bem_validation.pdf.gz | 489.9 KB | Display | wwPDB validaton report |
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Full document | 1bem_full_validation.pdf.gz | 500.6 KB | Display | |
Data in XML | 1bem_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1bem_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1bem ftp://data.pdbj.org/pub/pdb/validation_reports/be/1bem | HTTPS FTP |
-Related 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: 33168.844 Da / Num. of mol.: 1 / Mutation: MET ILE ADDED AT N-TERMINUS, W191Q Source method: isolated from a genetically manipulated source Details: A MES ION BOUND IN THE PROXIMAL REGION Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PUC8 / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-MES / |
#4: Water | ChemComp-HOH / |
Compound details | THE MUTATION DESTABILIZES THE 191 LOOP. IN MES BUFFER, A MOLECULE OF MES BINDS TO THE ENZYME, ...THE MUTATION DESTABILIZ |
Sequence details | THIS CYTOCHROME C PEROXIDASE DIFFERS FROM A PREVIOUSLY DEPOSITED STRUCTURE (PROTEIN DATA BANK ENTRY ...THIS CYTOCHROME |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 54 % |
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Crystal grow | Details: 100 MM MES/TRIS; 30% MPD |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Date: Nov 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→20 Å / σ(F): 0 Details: COORDINATES FOR RESIDUES -1, 0, AND 1 - 3 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. WATER MOLECULES WITH B-FACTORS ...Details: COORDINATES FOR RESIDUES -1, 0, AND 1 - 3 ARE NOT INCLUDED IN THIS ENTRY BECAUSE THESE RESIDUES COULD NOT BE RESOLVED IN THE FINAL ELECTRON DENSITY MAPS. WATER MOLECULES WITH B-FACTORS GREATER THAN 80 WERE NOT INCLUDED IN THE MODEL.
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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