[English] 日本語
Yorodumi- PDB-1ycc: HIGH-RESOLUTION REFINEMENT OF YEAST ISO-1-CYTOCHROME C AND COMPAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ycc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | HIGH-RESOLUTION REFINEMENT OF YEAST ISO-1-CYTOCHROME C AND COMPARISONS WITH OTHER EUKARYOTIC CYTOCHROMES C | |||||||||
Components | CYTOCHROME C | |||||||||
Keywords | ELECTRON TRANSPORT (CYTOCHROME) | |||||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity / heme binding ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / 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: 1.23 Å | |||||||||
Authors | Louie, G.V. / Brayer, G.D. | |||||||||
Citation | 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. #1: 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. #2: 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. #3: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ycc.cif.gz | 34.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ycc.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ycc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ycc_validation.pdf.gz | 484 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ycc_full_validation.pdf.gz | 489.5 KB | Display | |
Data in XML | 1ycc_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | 1ycc_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1ycc ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1ycc | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUE LYS 72 AND TML 72 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 5 ABOVE. |
-Components
#1: Protein | Mass: 12115.915 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00044 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEC / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.68 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.2 / Method: free interface diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.23 Å / Lowest resolution: 6 Å / Num. obs: 27713 / Observed criterion σ(F): 3 / Num. measured all: 48466 / Rmerge(I) obs: 0.081 |
---|
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor obs: 0.192 / Highest resolution: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / Num. reflection obs: 12513 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |