+Open data
-Basic information
Entry | Database: PDB / ID: 5o10 | ||||||
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Title | Y48H mutant of human cytochrome c | ||||||
Components | Cytochrome c | ||||||
Keywords | ELECTRON TRANSFER / APOPTOSIS / Heme / haem / cytochrome c / metalloprotein | ||||||
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: 1.36 Å | ||||||
Authors | Moreno-Chicano, T. / Deacon, O.M. / Hough, M.A. / Worrall, J.A.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Heightened Dynamics of the Oxidized Y48H Variant of Human Cytochrome c Increases Its Peroxidatic Activity. Authors: Deacon, O.M. / Karsisiotis, A.I. / Moreno-Chicano, T. / Hough, M.A. / Macdonald, C. / Blumenschein, T.M.A. / Wilson, M.T. / Moore, G.R. / Worrall, J.A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o10.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o10.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 5o10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/5o10 ftp://data.pdbj.org/pub/pdb/validation_reports/o1/5o10 | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11615.556 Da / Num. of mol.: 2 / Mutation: Y48H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYCS, CYC Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P99999 #2: Chemical | #3: 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: 2.43 Å3/Da / Density % sol: 49.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 33% PEG 6000 100mM Tris pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2016 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→54.25 Å / Num. obs: 45812 / % possible obs: 95.3 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Net I/av σ(I): 13.3 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.36→1.39 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2124 / CC1/2: 0.51 / Rpim(I) all: 0.51 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3zcf Resolution: 1.36→54.25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.963 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.052 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.31 Å2 / Biso mean: 18.567 Å2 / Biso min: 8.26 Å2
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Refinement step | Cycle: final / Resolution: 1.36→54.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.362→1.397 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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