+Open data
-Basic information
Entry | Database: PDB / ID: 4i7j | ||||||
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Title | T4 Lysozyme L99A/M102H with benzene bound | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE | ||||||
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 / PHENIX / Resolution: 1.67 Å | ||||||
Authors | Merski, M. / Shoichet, B.K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: The impact of introducing a histidine into an apolar cavity site on docking and ligand recognition. Authors: Merski, M. / 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 | 4i7j.cif.gz | 157.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i7j.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 4i7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/4i7j ftp://data.pdbj.org/pub/pdb/validation_reports/i7/4i7j | HTTPS FTP |
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-Related structure data
Related structure data | 4i7kC 4i7lC 4i7mC 4i7nC 4i7oC 4i7pC 4i7qC 4i7rC 4i7sC 4i7tC 4e97S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21404.426 Da / Num. of mol.: 2 Mutation: T21C, S38D, L99A, M102H, E108V, S117V, T142C, N144D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme |
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-Non-polymers , 6 types, 282 molecules
#2: Chemical | ChemComp-BME / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-HED / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: two flat Si(111) crystals, mounted in a model DCM from Khozu Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.67→48.311 Å / Num. obs: 40938 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.954 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.71 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: PHENIX Starting model: PDB ENTRY 4E97 Resolution: 1.67→48.311 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8352 / SU ML: 0.46 / σ(F): 1.99 / Phase error: 24.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.013 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.55 Å2 / Biso mean: 13.6937 Å2 / Biso min: 0.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→48.311 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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