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Yorodumi- PDB-2aiu: Crystal Structure of Mouse Testicular Cytochrome C at 1.6 Angstrom -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aiu | ||||||
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Title | Crystal Structure of Mouse Testicular Cytochrome C at 1.6 Angstrom | ||||||
Components | Cytochrome c, testis-specific | ||||||
Keywords | ELECTRON TRANSPORT / Cytochrome C / Mouse / Testis | ||||||
Function / homology | Function and homology information mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / hydrogen peroxide metabolic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / positive regulation of intrinsic apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / apoptotic process / heme binding ...mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / hydrogen peroxide metabolic process / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / positive regulation of intrinsic apoptotic signaling pathway / mitochondrial intermembrane space / electron transfer activity / apoptotic process / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Liu, Z. / Ye, S. / Lin, H. / Rao, Z. / Liu, X.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis Authors: Liu, Z. / Lin, H. / Ye, S. / Liu, Q.Y. / Meng, Z. / Zhang, C.M. / Xia, Y. / Margoliash, E. / Rao, Z. / Liu, X.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aiu.cif.gz | 35.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aiu.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 2aiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/2aiu ftp://data.pdbj.org/pub/pdb/validation_reports/ai/2aiu | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11734.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBTR1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P00015 | ||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: 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: 1.9 Å3/Da / Density % sol: 36.2 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: PEG1000, potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 8, 2005 |
Radiation | Monochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 12001 / Num. obs: 12001 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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