+Open data
-Basic information
Entry | Database: PDB / ID: 4xv7 | |||||||||||||||
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Title | CcP gateless cavity | |||||||||||||||
Components | Cytochrome c peroxidase, mitochondrial | |||||||||||||||
Keywords | OXIDOREDUCTASE / Model system / flexibility / thermodynamics / cryptic site / transient protein sites / ligand binding | |||||||||||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / peroxidase activity / response to reactive oxygen species / hydrogen peroxide catabolic process / mitochondrial intermembrane space / cellular response to oxidative stress / mitochondrial matrix / heme binding / mitochondrion / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å | |||||||||||||||
Authors | Fischer, M. / Fraser, J.S. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Chembiochem / Year: 2015 Title: One Crystal, Two Temperatures: Cryocooling Penalties Alter Ligand Binding to Transient Protein Sites. Authors: Fischer, M. / Shoichet, B.K. / Fraser, J.S. #1: Journal: Nat Chem / Year: 2014 Title: Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Authors: Fischer, M. / Coleman, R.G. / Fraser, J.S. / 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 | 4xv7.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xv7.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/4xv7 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/4xv7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological assembly is a monomer |
-Components
#1: Protein | Mass: 33290.062 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-362, NUMBERED 4-292 / Mutation: P190G, W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CCP1, CCP, CPO, YKR066C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00431, cytochrome-c peroxidase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-1LQ / |
#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: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Compound soaked into crystal grown in equal volume of 500mM MES buffer and 25% MPD |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95372 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2011 |
Radiation | Monochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→39.74 Å / Num. obs: 54914 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.95 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→39.74 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→39.74 Å
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Refine LS restraints |
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LS refinement shell |
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