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Yorodumi- PDB-4nfg: K13R mutant of horse cytochrome c and yeast cytochrome c peroxida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nfg | ||||||
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Title | K13R mutant of horse cytochrome c and yeast cytochrome c peroxidase complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
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 / : / response to reactive oxygen species ...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 / : / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / peroxidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Meulenbroek, E.M. / Bashir, Q. / Ubbink, M. / Pannu, N.S. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Engineering specificity in a dynamic protein complex with a single conserved mutation. Authors: Bashir, Q. / Meulenbroek, E.M. / Pannu, N.S. / Ubbink, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nfg.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nfg.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 4nfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nfg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4nfg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4nfg_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 4nfg_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/4nfg ftp://data.pdbj.org/pub/pdb/validation_reports/nf/4nfg | HTTPS FTP |
-Related structure data
Related structure data | 2pccS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 33601.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Protein | Mass: 11705.523 Da / Num. of mol.: 1 / Mutation: K13R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: CYCS, CYC / Production host: Escherichia coli (E. coli) / References: UniProt: P00004 |
-Non-polymers , 4 types, 305 molecules
#3: Chemical | ChemComp-HEM / |
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#4: Chemical | ChemComp-UNX / |
#5: Chemical | ChemComp-HEC / |
#6: 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: 2.28 Å3/Da / Density % sol: 45.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% PEG 3350, 150 mM NaCl, 0.5 mM 1:1 ratio of horse cytochrome c and yeast cytochrome c peroxidase, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 2010 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→52.37 Å / Num. all: 24499 / Num. obs: 24499 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PCC Resolution: 2.11→67.24 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.89 / SU B: 4.542 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.199 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→67.24 Å
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Refine LS restraints |
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