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Yorodumi- PDB-1ytc: THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ytc | |||||||||
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Title | THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIPS IN UNFOLDED PROTEINS | |||||||||
Components | YEAST ISO-2 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: 1.8 Å | |||||||||
Authors | Luo, Y. / Brayer, G.D. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Thermodynamic cycles as probes of structure in unfolded proteins. Authors: McGee, W.A. / Rosell, F.I. / Liggins, J.R. / Rodriguez-Ghidarpour, S. / Luo, Y. / Chen, J. / Brayer, G.D. / Mauk, A.G. / Nall, B.T. #1: Journal: Protein Sci. / Year: 1993 Title: The Structure and Function of Omega Loop a Replacements in Cytochrome C Authors: Murphy, M.E.P. / Fetrow, J.S. / Burton, R.E. / Brayer, G.D. #2: 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.P. / Nall, B.T. / Brayer, G.D. | |||||||||
History |
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Remark 700 | SHEET THE PDB HAS GENERATED THE HELIX AND SHEET RECORDS FROM THE COORDINATES USING A PROGRAM BASED ...SHEET THE PDB HAS GENERATED THE HELIX AND SHEET RECORDS FROM THE COORDINATES USING A PROGRAM BASED ON DSSP OF W. KABSCH AND C. SANDER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ytc.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ytc.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ytc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/1ytc ftp://data.pdbj.org/pub/pdb/validation_reports/yt/1ytc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12465.292 Da / Num. of mol.: 1 / Mutation: N52I Source method: isolated from a genetically manipulated source Details: REDUCED STATE OF HEME Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.5 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 24, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→69.5 Å / Num. obs: 9141 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.06 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 59573 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 93.4 % |
-Processing
Software |
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Refinement | Resolution: 1.8→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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