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Yorodumi- PDB-1cif: STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL... -
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-Basic information
Entry | Database: PDB / ID: 1cif | |||||||||
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Title | STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN 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: 1.9 Å | |||||||||
Authors | Lo, T.P. / Brayer, G.D. | |||||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structural and functional effects of multiple mutations at distal sites in cytochrome c. Authors: Lo, T.P. / Komar-Panicucci, S. / Sherman, F. / McLendon, G. / Brayer, G.D. #1: Journal: J.Mol.Biol. / Year: 1994 Title: The Role of a Conserved Internal Water Molecule and its Associated Hydrogen Bond Network in Cytochrome C Authors: Berghuis, A.M. / Guillemette, J.G. / Mclendon, G. / Sherman, F. / Brayer, G.D. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Mutation of Tyrosine-67 to Phenylalanine in Cytochrome C Significantly Alters the Local Heme Environment Authors: Berghuis, A.M. / Guillemette, J.G. / Smith, M. / Brayer, G.D. #3: Journal: J.Mol.Biol. / Year: 1992 Title: Oxidation State-Dependent Conformational Changes in Cytochrome C Authors: Berghuis, A.M. / Brayer, G.D. #4: 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. #5: 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. #6: 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. #7: 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. #8: 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. | |||||||||
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 | 1cif.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cif.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1cif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/1cif ftp://data.pdbj.org/pub/pdb/validation_reports/ci/1cif | 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 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 ...2: 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. RESIDUE LYS 72 IS TRIMETHYLATED AT THE AMINO END OF ITS SIDE CHAIN. 3: RESIDUES MET 80 AND HIS 18 FORM HEME IRON LIGAND BONDS. |
-Components
#1: Protein | Mass: 11937.637 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 AN ALANINE RESIDUE. ...THIS PROTEIN HAS BEEN STABILIZED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.9 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 7030 / Num. measured all: 22149 / Rmerge(I) obs: 0.091 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |