[English] 日本語
Yorodumi- PDB-1csx: REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1csx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF 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 / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / : / mitochondrial intermembrane space / electron transfer activity ...Release of apoptotic factors from the mitochondria / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / cardiolipin binding / 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 | Lo, T.P. / Brayer, G.D. | |||||||||
Citation | Journal: Protein Sci. / Year: 1995 Title: Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c. Authors: Lo, T.P. / Murphy, M.E. / Guillemette, J.G. / Smith, M. / Brayer, G.D. #1: Journal: Biochemistry / Year: 1995 Title: Structural Studies of the Roles of Residues 82 and 85 at the Interactive Face of Cytochrome C Authors: Lo, T.P. / Guillemette, J.G. / Louie, G.V. / Smith, M. / Brayer, G.D. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Oxidation State-Dependent Conformational Changes in Cytochrome C Authors: Berghuis, A.M. / Brayer, G.D. #3: 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. #4: 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. #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. #6: 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. #7: 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 | 1csx.cif.gz | 34 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1csx.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1csx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1csx_validation.pdf.gz | 489.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1csx_full_validation.pdf.gz | 497.4 KB | Display | |
Data in XML | 1csx_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1csx_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/1csx ftp://data.pdbj.org/pub/pdb/validation_reports/cs/1csx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: THE HEME GROUP IS COVALENTLY ATTACHED TO THE PROTEIN VIA THIOETHER BONDS FROM THE SG ATOMS OF CYS 14 AND CYS 17, TO THE CAB AND CAC HEME ATOMS, RESPECTIVELY. 2: RESIDUE 72 IS EPSILON-N-TRIMETHYLLYSINE. THE THREE METHYL CARBONS FOR THIS RESIDUE ARE PRESENT AS HETATMS WITH RESIDUE NAME TML (FOLLOWING THE HEME). RESIDUE 72 IS IDENTIFIED AS LYS ON THE ATOM ...2: RESIDUE 72 IS EPSILON-N-TRIMETHYLLYSINE. THE THREE METHYL CARBONS FOR THIS RESIDUE ARE PRESENT AS HETATMS WITH RESIDUE NAME TML (FOLLOWING THE HEME). RESIDUE 72 IS IDENTIFIED AS LYS ON THE ATOM AND SEQRES RECORDS. RESIDUE LYS 72 IS TRIMETHYLATED AT THE AMINO END OF ITS SIDE CHAIN. 3: RESIDUES MET 80 AND HIS 18 FORM HEME IRON LIGAND BONDS. |
-Components
#1: Protein | Mass: 12087.796 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.86 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6.7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→6 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|