+Open data
-Basic information
Entry | Database: PDB / ID: 2rbo | ||||||
---|---|---|---|---|---|---|---|
Title | 2-nitrothiophene in complex with T4 lysozyme L99A/M102Q | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2rbo.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2rbo.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2rbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/2rbo ftp://data.pdbj.org/pub/pdb/validation_reports/rb/2rbo | HTTPS FTP |
---|
-Related structure data
Related structure data | 2rayC 2razC 2rb0C 2rb1C 2rb2C 2rbnC 2rbpC 2rbqC 2rbrC 2rbsC 2rbtC 2rbuC 2rbvC 2rbwC 2rbxC 2rbyC 2rbzC 2rc0C 2rc1C 2rc2C 1lguS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18390.061 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 / Gene: E / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-265 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979462 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2006 Details: Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979462 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→52.06 Å / Num. all: 51583 / Num. obs: 51583 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.29→1.34 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.622 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LGU Resolution: 1.29→52.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.272 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.447 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→52.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.29→1.324 Å / Total num. of bins used: 20
|