+Open data
-Basic information
Entry | Database: PDB / ID: 2ycc | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | OXIDATION STATE-DEPENDENT CONFORMATIONAL CHANGES IN CYTOCHROME C | |||||||||
Components | CYTOCHROME C | |||||||||
Keywords | ELECTRON TRANSPORT (HEME PROTEIN) | |||||||||
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: 1.9 Å | |||||||||
Authors | Berghuis, A.M. / Brayer, G.D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1992 Title: Oxidation state-dependent conformational changes in cytochrome c. Authors: Berghuis, A.M. / Brayer, G.D. #1: 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. #2: 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. #3: 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. #4: 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. #5: 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 |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ycc.cif.gz | 34.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ycc.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ycc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ycc_validation.pdf.gz | 795.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ycc_full_validation.pdf.gz | 808.2 KB | Display | |
Data in XML | 2ycc_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 2ycc_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/2ycc ftp://data.pdbj.org/pub/pdb/validation_reports/yc/2ycc | HTTPS FTP |
-Related structure data
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 8 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 REDUCED AND OXIDIZED FORMS OF YEAST ISO-1 CYTOCHROME C (PROTEIN DATA BANK ENTRIES 1YCC AND 2YCC, RESPECTIVELY), ...3: IN ORDER TO CORRECTLY INDICATE IDENTICAL ATOMS BETWEEN THE COORDINATE ENTRIES OF THE REDUCED AND OXIDIZED FORMS OF YEAST ISO-1 CYTOCHROME C (PROTEIN DATA BANK ENTRIES 1YCC AND 2YCC, 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, GLU 21, ARG 38, GLU 44, TYR 46, ASP 50, GLU 61, TYR 67, PHE 82, AND ASP 90. | ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 12113.876 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00044 |
---|---|
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.9 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.7 / Method: vapor diffusion, hanging drop / Details: took from Sherwood & Brayer from original paper | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Num. measured all: 8632 |
---|
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor obs: 0.197 / Highest resolution: 1.9 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 3929 / σ(F): 2 / Rfactor obs: 0.197 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
|