+Open data
-Basic information
Entry | Database: PDB / ID: 1ov5 | ||||||
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Title | T4 Lysozyme Cavity Mutant L99a/M102Q Bound With 2-Allylphenol | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wei, B.Q. / Baase, W.A. / Weaver, L.H. / Matthews, B.W. / Shoichet, B.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Testing a Flexible-receptor Docking Algorithm in a Model Binding Site Authors: Wei, B.Q. / Weaver, L.H. / Ferrari, A.M. / Matthews, B.W. / Shoichet, B.K. #1: Journal: J.Mol.Biol. / Year: 2002 Title: A Model Binding Site for Testing Scoring Functions in Molecular Docking Authors: Wei, B.Q. / Baase, W.A. / Weaver, L.H. / Matthews, B.W. / 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 | 1ov5.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ov5.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ov5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ov5_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 1ov5_full_validation.pdf.gz | 452 KB | Display | |
Data in XML | 1ov5_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1ov5_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/1ov5 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/1ov5 | HTTPS FTP |
-Related structure data
Related structure data | 1ov7C 1ovhC 1ovjC 1ovkC 1owyC 1owzC 1lguS 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: 18617.320 Da / Num. of mol.: 1 / Mutation: L99A, M102Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-2LP / | #4: Chemical | #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: 2.7 Å3/Da / Density % sol: 54.05 % |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: UCSD MARK II / Detector: AREA DETECTOR / Date: Dec 1, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→13 Å / Num. obs: 8950 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.1→2.26 Å / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1145 / % possible all: 52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LGU Resolution: 2.1→13 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 2.1→13 Å
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Refine LS restraints |
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