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Yorodumi- PDB-4nvi: Predicting protein conformational response in prospective ligand ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nvi | ||||||
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Title | Predicting protein conformational response in prospective ligand discovery. | ||||||
Components | Cytochrome c peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Model system / flexibility / dynamic / loop / side-chains / energy penalty / occupancy / Boltzmann weights / flexible docking / ligand binding | ||||||
Function / homology | Function and homology information cytochrome-c peroxidase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / cellular response to oxidative stress / mitochondrial matrix / heme binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å | ||||||
Authors | Fischer, M. / Fraser, J.S. | ||||||
Citation | 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 | 4nvi.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nvi.ent.gz | 120.1 KB | Display | PDB format |
PDBx/mmJSON format | 4nvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/4nvi ftp://data.pdbj.org/pub/pdb/validation_reports/nv/4nvi | HTTPS FTP |
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-Related structure data
Related structure data | 4nvaC 4nvbC 4nvcC 4nvdC 4nveC 4nvfC 4nvgC 4nvhC 4nvjC 4nvkC 4nvlC 4nvmC 4nvnC 4nvoC 4oq7C 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: 32928.582 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-362 / Mutation: P190G, W191G, DELETIONS G192-A193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: RM11-1A / Gene: CCP1 CCP CPO YKR066C, SCRG_04081 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3LRE1 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-2NW / | ||
#4: Chemical | ChemComp-PO4 / #5: 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: 2.95 Å3/Da / Density % sol: 58.33 % |
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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 (pH 6.0) and 25% MPD, vapor diffusion, hanging drop, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2012 |
Radiation | Monochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→31.4 Å / Num. all: 61321 / Num. obs: 61321 / % possible obs: 99.1 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 2.2 / Redundancy: 4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.51→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4240 / % possible all: 97.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→31.4 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9078 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 15.87 / 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 max: 57.82 Å2 / Biso mean: 20.8295 Å2 / Biso min: 8.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→31.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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