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Yorodumi- PDB-1yeb: STRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yeb | |||||||||
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Title | STRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN | |||||||||
Components | CYTOCHROME C | |||||||||
Keywords | ELECTRON TRANSPORT | |||||||||
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: 1.95 Å | |||||||||
Authors | Murphy, M.E.P. / Brayer, G.D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Structure determination and analysis of yeast iso-2-cytochrome c and a composite mutant protein. Authors: Murphy, M.E. / 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 | 1yeb.cif.gz | 32.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yeb.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1yeb ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1yeb | 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 7. |
-Components
#1: Protein | Mass: 12123.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00045 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.58 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.2 / Method: vapor diffusion, hanging drop / Details: hair seeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.95 Å / Num. obs: 7352 / Num. measured all: 10866 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.95→6 Å / Rfactor obs: 0.175 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.95 Å / Lowest resolution: 6 Å / σ(F): 2 / Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.5 Å2 |