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Yorodumi- PDB-1cty: MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE ... -
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-Basic information
Entry | Database: PDB / ID: 1cty | |||||||||
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Title | MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE LOCAL HEME ENVIRONMENT | |||||||||
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: 2.2 Å | |||||||||
Authors | Berghuis, A.M. / Brayer, G.D. | |||||||||
Citation | 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. #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 | 1cty.cif.gz | 33.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cty.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 1cty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/1cty ftp://data.pdbj.org/pub/pdb/validation_reports/ct/1cty | 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: RESIDUE LYS 72 AND TML 72 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 9 ABOVE. 2: THE HEME GROUP IS COVALENTLY ATTACHED TO THE PROTEIN VIA THIOETHER BONDS TO THE SG ATOMS OF CYS 14 AND CYS 17. 3: IN ORDER TO CORRECTLY INDICATE IDENTICAL ATOMS BETWEEN THE COORDINATE ENTRIES OF THE MUTANT AND WILD-TYPE FORMS OF YEAST ISO-1 CYTOCHROME C (PROTEIN DATA BANK ENTRIES 1CTY AND 1YCC, RESPECTIVELY), ...3: IN ORDER TO CORRECTLY INDICATE IDENTICAL ATOMS BETWEEN THE COORDINATE ENTRIES OF THE MUTANT AND WILD-TYPE FORMS OF YEAST ISO-1 CYTOCHROME C (PROTEIN DATA BANK ENTRIES 1CTY AND 1YCC, RESPECTIVELY), THE SIDE-CHAIN ATOM NAMES OF SEVERAL RESIDUES CANNOT FOLLOW IUPAC/IUB SPECIFICATIONS WITH RESPECT TO THE DESIGNATION OF 1 AND 2 FOR BRANCHED SIDE CHAINS. THE AFFECTED RESIDUES ARE GLU -4, PHE -3, PHE 10, ARG 38, TYR 46, TYR 48, ASP 50, PHE 67, PHE 82, ASP 90, AND GLU 103. |
-Components
#1: Protein | Mass: 12097.876 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: 1.92 Å3/Da / Density % sol: 35.85 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: using a hair-seeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.196 / Highest resolution: 2.2 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Rfactor obs: 0.196 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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