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Yorodumi- PDB-1chi: STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTE... -
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-Basic information
Entry | Database: PDB / ID: 1chi | |||||||||
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Title | STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C | |||||||||
Components | CYTOCHROME C | |||||||||
Keywords | ELECTRON TRANSPORT(HEME PROTEIN) | |||||||||
Function / homology | Function and homology information Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding ...Pyroptosis / Release of apoptotic factors from the mitochondria / Detoxification of Reactive Oxygen Species / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Lo, T.P. / Brayer, G.D. | |||||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structural studies of the roles of residues 82 and 85 at the interactive face of cytochrome c. Authors: Lo, T.P. / Guillemette, J.G. / Louie, G.V. / Smith, M. / Brayer, G.D. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Oxidation State-Dependent Conformational Changes in Cytochrome C Authors: Berghuis, A.M. / Brayer, G.D. #2: Journal: J.Mol.Biol. / Year: 1990 Title: High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C Authors: Louie, G.V. / Brayer, G.D. #3: Journal: J.Mol.Biol. / Year: 1989 Title: A Polypeptide Chain-Refolding Event Occurs in the Gly82 Variant of Yeast Iso-1-Cytochrome C Authors: Louie, G.V. / Brayer, G.D. #4: Journal: J.Mol.Biol. / Year: 1989 Title: Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique Authors: Leung, C.J. / Nall, B.T. / Brayer, G.D. #5: Journal: J.Mol.Biol. / Year: 1988 Title: Yeast Iso-1-Cytochrome C. A 2.8 Angstrom Resolution Three-Dimensional Structure Determination Authors: Louie, G.V. / Hutcheon, W.L.B. / Brayer, G.D. #6: Journal: Biochemistry / Year: 1988 Title: Role of Phenylalanine-82 in Yeast Iso-1-Cytochrome C and Remote Conformational Changes Induced by a Serine Residue at This Position Authors: Louie, G.V. / Pielak, G.J. / Smith, M. / Brayer, G.D. | |||||||||
History |
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Remark 650 | HELIX THE END OF THE 50 HELIX (RESIDUE 55) IS DISTORTED. | |||||||||
Remark 700 | SHEET RESIDUES IN SHEET S1 FORM A HIGHLY DISTORTED BETA TYPE CONFORMATION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1chi.cif.gz | 34.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1chi.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 1chi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/1chi ftp://data.pdbj.org/pub/pdb/validation_reports/ch/1chi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THE HEME GROUP IS COVALENTLY ATTACHED TO THE PROTEIN VIA THIOETHER BONDS FROM THE SG ATOMS OF CYS 14 AND CYS 17, TO THE CAB AND CAC HEME ATOMS, RESPECTIVELY. 2: RESIDUE LYS 72 IS TRIMETHYLATED AT THE AMINO END OF ITS SIDE CHAIN. RESIDUE 72 IS EPSILON-N-TRIMETHYLLYSINE. THE THREE METHYL CARBONS FOR THIS RESIDUE ARE PRESENT AS HETATMS WITH RESIDUE NAME TML ...2: RESIDUE LYS 72 IS TRIMETHYLATED AT THE AMINO END OF ITS SIDE CHAIN. RESIDUE 72 IS EPSILON-N-TRIMETHYLLYSINE. THE THREE METHYL CARBONS FOR THIS RESIDUE ARE PRESENT AS HETATMS WITH RESIDUE NAME TML (FOLLOWING THE HEME). RESIDUE 72 IS IDENTIFIED AS LYS ON THE ATOM AND SEQRES RECORDS. 3: RESIDUES MET 80 AND HIS 18 FORM HEME IRON LIGAND BONDS. |
-Components
#1: Protein | Mass: 12087.796 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00044 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEC / |
#4: Water | ChemComp-HOH / |
Compound details | THIS PROTEIN HAS BEEN STABILIZED FOR ANALYSES BY THE MUTATION OF CYSTEINE 102 TO A THREONINE ...THIS PROTEIN HAS BEEN STABILIZED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.98 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. measured all: 6823 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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