+Open data
-Basic information
Entry | Database: PDB / ID: 5u5z | ||||||
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Title | CcP gateless cavity | ||||||
Components | Peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Model system / Cytochrome c Peroxidase / GIST / desolvation / 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: 1.26 Å | ||||||
Authors | Fischer, M. / Shoichet, B.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Testing inhomogeneous solvation theory in structure-based ligand discovery. Authors: Balius, T.E. / Fischer, M. / Stein, R.M. / Adler, T.B. / Nguyen, C.N. / Cruz, A. / Gilson, M.K. / Kurtzman, T. / Shoichet, B.K. #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 | 5u5z.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u5z.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 5u5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u5z_validation.pdf.gz | 797 KB | Display | wwPDB validaton report |
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Full document | 5u5z_full_validation.pdf.gz | 797.8 KB | Display | |
Data in XML | 5u5z_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5u5z_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/5u5z ftp://data.pdbj.org/pub/pdb/validation_reports/u5/5u5z | HTTPS FTP |
-Related structure data
Related structure data | 5u5uC 5u5vC 5u5wC 5u5xC 5u5yC 5u60C 5u61C 5ug2C 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 / Mutation: P190G, W191G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast) Strain: RM11-1a / Gene: SCRG_04081 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B3LRE1, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-7VP / |
#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: 58.08 % / Mosaicity: 0 ° |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 13, 2016 | ||||||||||||||||||
Radiation | Monochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.26→73.24 Å / Num. obs: 90514 / % possible obs: 84.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 14.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Net I/σ(I): 14.8 / Num. measured all: 1022444 / Scaling rejects: 460 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→52.414 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.32 Å2 / Biso mean: 20.3868 Å2 / Biso min: 9.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.26→52.414 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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