+Open data
-Basic information
Entry | Database: PDB / ID: 2ray | ||||||
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Title | beta-chlorophenetole in complex with T4 lysozyme L99A | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / protein cavities | ||||||
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 / Resolution: 1.798 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 | 2ray.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ray.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ray.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/2ray ftp://data.pdbj.org/pub/pdb/validation_reports/ra/2ray | HTTPS FTP |
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-Related structure data
Related structure data | 2razC 2rb0C 2rb1C 2rb2C 2rbnC 2rboC 2rbpC 2rbqC 2rbrC 2rbsC 2rbtC 2rbuC 2rbvC 2rbwC 2rbxC 2rbyC 2rbzC 2rc0C 2rc1C 2rc2C 184lS C: citing same article (ref.) S: Starting model for refinement |
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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: 18359.023 Da / Num. of mol.: 1 / Mutation: L99A 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 / Gene: E / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-258 / ( |
#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: 2.76 Å3/Da / Density % sol: 55.41 % |
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Crystal grow | Temperature: 277 K / Method: hanging drop / pH: 7.1 Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 26, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→52.34 Å / Num. all: 19492 / Num. obs: 19434 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.798→1.84 Å / % possible all: 98.9 |
-Processing
Software |
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Refinement | Starting model: 184L Resolution: 1.798→52.34 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.374 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.111 / 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: 20.548 Å2
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Refinement step | Cycle: LAST / Resolution: 1.798→52.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.798→1.844 Å / Total num. of bins used: 20
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