[English] 日本語
![](img/lk-miru.gif)
- PDB-1irv: CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY M... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1irv | ||||||
---|---|---|---|---|---|---|---|
Title | CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY MET AND CYS 102 REPLACED BY THR | ||||||
![]() | CYTOCHROME C | ||||||
![]() | ELECTRON TRANSPORT / HEME PROTEIN / MITOCHONDRION | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Berghuis, A.M. / Brayer, G.D. | ||||||
![]() | ![]() Title: Mechanistic and structural contributions of critical surface and internal residues to cytochrome c electron transfer reactivity. Authors: Rafferty, S.P. / Guillemette, J.G. / Berghuis, A.M. / Smith, M. / Brayer, G.D. / Mauk, A.G. #1: ![]() Title: The Role of a Conserved Internal Water Molecule and its Associated Hydrogen Bond Network in Cytochrome C Authors: Berghuis, A.M. / Guillemette, J.G. / Mclendon, G. / Sherman, F. / Smith, M. / Brayer, G.D. #2: ![]() Title: Mutation of Tyrosine-67 to Phenylalanine in Cytochrome C Significantly Alters the Local Heme Environment Authors: Berghuis, A.M. / Guillemette, J.G. / Smith, M. / Brayer, G.D. #3: ![]() Title: Oxidation State-Dependent Conformational Changes in Cytochrome C Authors: Berghuis, A.M. / Brayer, G.D. #4: ![]() Title: High-Resolution Refinement of Yeast Iso-1-Cytochrome C and Comparisons with Other Eukaryotic Cytochromes C Authors: Louie, G.V. / Brayer, G.D. #5: ![]() Title: Crystallization of Yeast Iso-2-Cytochrome C Using a Novel Hair Seeding Technique Authors: Leung, C.J. / Nall, B.T. / Brayer, G.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 33.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 25 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 788.7 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 12131.914 Da / Num. of mol.: 1 / Mutation: I75M, C102T Source method: isolated from a genetically manipulated source Details: ISOZYME 1, REDUCED Source: (gene. exp.) ![]() ![]() References: UniProt: P00044 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 5.3 / Method: unknown / Details: macroseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 |
---|---|
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→6 Å / Num. obs: 8110 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 1 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→6 Å / σ(F): 2 Details: PROLSQ STANDARD SET OF IDEAL BOND LENGTHS ETC. (I.E. VERY SIMILAR TO ENGH & HUBER) ESTIMATED COORD. ERROR 0.25 ANGSTROMS FINAL RMS COORD. SHIFT 0.35 ANGSTROMS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.222 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |