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Yorodumi- PDB-2b4z: Crystal structure of cytochrome C from bovine heart at 1.5 A reso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b4z | ||||||
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Title | Crystal structure of cytochrome C from bovine heart at 1.5 A resolution. | ||||||
Components | Cytochrome c | ||||||
Keywords | ELECTRON TRANSPORT / FERRIC FORM / LOW IONIC STRENGTH | ||||||
Function / homology | Function and homology information Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / apoptotic process / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Mirkin, N. / Jakoncic, J. / Stojanoff, V. / Moreno, A. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: High resolution X-ray crystallographic structure of bovine heart cytochrome c and its application to the design of an electron transfer biosensor. Authors: Mirkin, N. / Jaconcic, J. / Stojanoff, V. / Moreno, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b4z.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b4z.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 2b4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/2b4z ftp://data.pdbj.org/pub/pdb/validation_reports/b4/2b4z | HTTPS FTP |
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-Related structure data
Related structure data | 1crcS 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: 11595.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mitochondrion, heart. / Source: (natural) Bos taurus (cattle) / Organ: HEART / References: UniProt: P62894 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.314 Å3/Da / Density % sol: 44.79 % |
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Crystal grow | Temperature: 277 K / Method: microseeding / pH: 7 Details: PEG 1000, SODIUM PHOSPHATE, pH 7.0, MICROSEEDING, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0332 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38 Å / Num. all: 18439 / Num. obs: 17207 / Biso Wilson estimate: 14.5 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CRC Resolution: 1.5→30.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 419151.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.873 Å2 / ksol: 0.37269 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→30.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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