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Yorodumi- PDB-2rc1: Cytochrome C Peroxidase W191G in complex with 2,4,5-trimethyl-3-o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rc1 | ||||||
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Title | Cytochrome C Peroxidase W191G in complex with 2,4,5-trimethyl-3-oxazoline | ||||||
Components | Cytochrome C Peroxidase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding ...cytochrome-c peroxidase / cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å | ||||||
Authors | Graves, A.P. / Boyce, S.E. / Shoichet, B.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Rescoring docking hit lists for model cavity sites: predictions and experimental testing. Authors: Graves, A.P. / Shivakumar, D.M. / Boyce, S.E. / Jacobson, M.P. / Case, D.A. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rc1.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rc1.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 2rc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rc1_validation.pdf.gz | 811.3 KB | Display | wwPDB validaton report |
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Full document | 2rc1_full_validation.pdf.gz | 814.6 KB | Display | |
Data in XML | 2rc1_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2rc1_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/2rc1 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rc1 | HTTPS FTP |
-Related structure data
Related structure data | 2rayC 2razC 2rb0C 2rb1C 2rb2C 2rbnC 2rboC 2rbpC 2rbqC 2rbrC 2rbsC 2rbtC 2rbuC 2rbvC 2rbwC 2rbxC 2rbyC 2rbzC 2rc0C 2rc2C 1ac4S S: Starting model for refinement C: citing same article (ref.) |
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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: 33198.867 Da / Num. of mol.: 1 / Mutation: W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: YJM789 / Gene: ccp1, ccp, cpo / Plasmid: PT7CCP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A7A026, UniProt: P00431*PLUS, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-285 / ( |
#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: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 291 K / pH: 6 Details: MES, MPD, pH 6.0, vapor diffusion, hanging drop, temperature 291K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2007 / Details: KOHZU: DOUBLE CRYSTAL SI(111) |
Radiation | Monochromator: KHOZU DOUBLE FLAT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115872 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→59.87 Å / Num. obs: 11612 / % possible obs: 53.7 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.49→2.59 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.059 / % possible all: 51.7 |
-Processing
Software |
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Refinement | Starting model: 1AC4 Resolution: 2.49→59.87 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.843 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.629 / ESU R Free: 0.29 / 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: 12.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→59.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.56 Å / Total num. of bins used: 20
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