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Open data
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Basic information
Entry | Database: PDB / ID: 2rbo | ||||||
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Title | 2-nitrothiophene in complex with T4 lysozyme L99A/M102Q | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / protein cavities | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Graves, A.P. / Boyce, S.E. / Shoichet, B.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.4 KB | Display | ![]() |
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PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.3 KB | Display | ![]() |
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Full document | ![]() | 441.4 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-265 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.14 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: LAST / Resolution: 1.29→52.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.29→1.324 Å / Total num. of bins used: 20
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