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Yorodumi- PDB-1irw: CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ASN 52 REPLACED BY A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1irw | ||||||
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Title | CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ASN 52 REPLACED BY ALA AND CYS 102 REPLACED BY THR | ||||||
Components | CYTOCHROME C | ||||||
Keywords | ELECTRON TRANSPORT / HEME PROTEIN / MITOCHONDRION | ||||||
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 | Berghuis, A.M. / Brayer, G.D. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Mechanistic and structural contributions of critical surface and internal residues to cytochrome c electron transfer reactivity. Authors: Rafferty, S.P. / Guillemette, J.G. / Berghuis, A.M. / Smith, M. / Brayer, G.D. / Mauk, A.G. #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. / Smith, M. / 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: Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique Authors: Leung, C.J. / Nall, B.T. / Brayer, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1irw.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1irw.ent.gz | 24.9 KB | Display | PDB format |
PDBx/mmJSON format | 1irw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/1irw ftp://data.pdbj.org/pub/pdb/validation_reports/ir/1irw | 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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-Components
#1: Protein | Mass: 12070.851 Da / Num. of mol.: 1 / Mutation: N52A, C102T Source method: isolated from a genetically manipulated source Details: ISOZYME 1, REDUCED Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00044 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.16 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.3 / Method: unknown / Details: macroseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 6933 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 1 % |
-Processing
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Refinement | Resolution: 2→6 Å / σ(F): 2 Details: PROLSQ STANDARD SET OF IDEAL BOND LENGTHS ETC. (I.E. VERY SIMILAR TO ENGH & HUBER) ESTIMATED COORD. ERROR 0.18 ANGSTROMS FINAL RMS COORD. SHIFT 0.27 ANGSTROMS
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Displacement parameters | Biso mean: 17.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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