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Yorodumi- PDB-5df5: The structure of oxidized rat cytochrome c (T28E) at 1.30 angstro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5df5 | ||||||
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Title | The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution. | ||||||
Components | Cytochrome c, somatic | ||||||
Keywords | ELECTRON TRANSPORT / cytochrome c / oxidized / rat / mutant | ||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Transcriptional activation of mitochondrial biogenesis / Pyroptosis / Respiratory electron transport / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / response to carbon monoxide / Cytoprotection by HMOX1 / apoptosome / Regulation of the apoptosome activity / negative regulation of hydrogen peroxide biosynthetic process / response to gravity / positive regulation of cellular respiration / glial cell apoptotic process / response to copper ion / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / hydrogen peroxide metabolic process / respirasome / response to ischemia / mitochondrial intermembrane space / response to oxidative stress / electron transfer activity / apoptotic process / heme binding / enzyme binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.301 Å | ||||||
Authors | Edwards, B.F.P. / Mahapatra, G. / Vaishnav, A.A. / Brunzelle, J.S. / Huttemann, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution. Authors: Edwards, B.F.P. / Mahapatra, G. / Vaishnav, A.A. / Brunzelle, J.S. / Huttemann, M. #1: Journal: Biochemistry / Year: 2010 Title: Phosphomimetic substitution of cytochrome C tyrosine 48 decreases respiration and binding to cardiolipin and abolishes ability to trigger downstream caspase activation. Authors: Pecina, P. / Borisenko, G.G. / Belikova, N.A. / Tyurina, Y.Y. / Pecinova, A. / Lee, I. / Samhan-Arias, A.K. / Przyklenk, K. / Kagan, V.E. / Huttemann, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5df5.cif.gz | 197.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5df5.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 5df5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/5df5 ftp://data.pdbj.org/pub/pdb/validation_reports/df/5df5 | HTTPS FTP |
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-Related structure data
Related structure data | 5c0zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11525.303 Da / Num. of mol.: 4 / Mutation: T28E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: somatic / Gene: Cycs / Plasmid: pLW01 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P62898 #2: Chemical | ChemComp-HEC / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | The sequence of this entry (rat Cytochrome c as found in UNP P62898/CYC_RAT) and and the mouse ...The sequence of this entry (rat Cytochrome c as found in UNP P62898/CYC_RAT) and and the mouse Cytochrome c (P62897/CYC_MOUSE) are identical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % / Description: 0.2 x 0.3 mm prism |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20 mg/mL protein in water mixed 1:1 with 30% PEG 1500 PH range: 4.5 only |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07812 Å / Relative weight: 1 |
Reflection | Resolution: 1.301→57.881 Å / Num. all: 95201 / Num. obs: 90455 / % possible obs: 96.59 % / Redundancy: 5.3 % / Biso Wilson estimate: 13.53 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.301→1.335 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 2.6 / % possible all: 89.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C0Z Resolution: 1.301→57.88 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.145 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.317 Å2
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Refinement step | Cycle: LAST / Resolution: 1.301→57.88 Å
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