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Yorodumi- PDB-1u75: Electron Transfer Complex between Horse Heart Cytochrome c and Zi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u75 | |||||||||
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Title | Electron Transfer Complex between Horse Heart Cytochrome c and Zinc-Porphyrin Substituted Cytochrome c Peroxidase | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / Protein-Protein Complex / Heme | |||||||||
Function / homology | Function and homology information cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / positive regulation of cysteine-type endopeptidase activity / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / peroxidase activity ...cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / positive regulation of cysteine-type endopeptidase activity / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / positive regulation of apoptotic process / lipid binding / apoptotic process / heme binding / mitochondrion / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Equus caballus (horse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | |||||||||
Authors | Crane, B.R. / Kang, S.A. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2004 Title: Electron transfer between cytochrome c and cytochome c peroxidase in single crystals. Authors: Kang, S.A. / Marjavaara, P.J. / Crane, B.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u75.cif.gz | 164.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u75.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 1u75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/1u75 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/1u75 | HTTPS FTP |
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-Related structure data
Related structure data | 1u74C 2pcbS C: citing same article (ref.) 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 1 - 294 / Label seq-ID: 3 - 296
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Details | The biological assembly is a trimer containing two molecules of cytochrome c peroxidase and one molecule of cytochrome c |
-Components
-Protein , 2 types, 3 molecules ACB
#1: Protein | Mass: 33769.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Yeast / Plasmid: pT7CCP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 171177, UniProt: P00431*PLUS, cytochrome-c peroxidase #2: Protein | | Mass: 11725.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Horse Heart / Source: (natural) Equus caballus (horse) / References: UniProt: P00004 |
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-Non-polymers , 4 types, 325 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-HEC / | #6: 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: 3.19 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 78 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9363 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2003 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9363 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 132655 / Num. obs: 34216 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.55→2.64 Å / Mean I/σ(I) obs: 3.9 / Num. unique all: 3312 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PCB Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.886 / SU B: 29.815 / SU ML: 0.326 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.605 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.565 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.55→2.615 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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