+Open data
-Basic information
Entry | Database: PDB / ID: 5ty3 | ||||||
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Title | Crystal structure of K72A variant of Human Cytochrome c | ||||||
Components | Cytochrome c | ||||||
Keywords | ELECTRON TRANSPORT / Human Cytochrome c / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...Formation of apoptosome / apoptosome / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / Release of apoptotic factors from the mitochondria / Respiratory electron transport / cellular respiration / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / Detoxification of Reactive Oxygen Species / Pyroptosis / respirasome / intrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / Cytoprotection by HMOX1 / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Mou, T.C. / Nold, S.M. / Lei, H. / Sprang, S.R. / Bowler, B.E. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Effect of a K72A Mutation on the Structure, Stability, Dynamics, and Peroxidase Activity of Human Cytochrome c. Authors: Nold, S.M. / Lei, H. / Mou, T.C. / Bowler, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ty3.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ty3.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ty3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/5ty3 ftp://data.pdbj.org/pub/pdb/validation_reports/ty/5ty3 | HTTPS FTP |
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-Related structure data
Related structure data | 3zcfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11582.479 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYCS, CYC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P99999 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 50.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG 6000, 0.1 M TRIS PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.07 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2016 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→23.83 Å / Num. obs: 62478 / % possible obs: 97.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.85 Å2 / Rsym value: 0.07 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.25→1.29 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 6.1 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZCF Resolution: 1.25→23.83 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→23.83 Å
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Refine LS restraints |
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LS refinement shell |
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