+Open data
-Basic information
Entry | Database: PDB / ID: 5jwt | ||||||
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Title | T4 Lysozyme L99A/M102Q with Benzene Bound | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / Phage lysozyme Azaborine | ||||||
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: 1.41 Å | ||||||
Authors | Lee, H. / Fischer, M. / Shoichet, B.K. / Liu, S.-Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics. Authors: Lee, H. / Fischer, M. / Shoichet, B.K. / Liu, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jwt.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jwt.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/5jwt ftp://data.pdbj.org/pub/pdb/validation_reports/jw/5jwt | HTTPS FTP |
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-Related structure data
Related structure data | 5jwsC 5jwuC 5jwvC 5jwwC 1lguS 5jwx 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: 18646.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-BNZ / |
#3: 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: 2.77 Å3/Da / Density % sol: 55.65 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 2.2 M sodium/potassium phosphate, pH 6.9, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2015 |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→45.926 Å / Num. obs: 39667 / % possible obs: 99.6 % / Redundancy: 8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 2.9 |
Reflection shell | Resolution: 1.41→1.46 Å / Rmerge(I) obs: 0.321 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LGU Resolution: 1.41→45.926 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.05 Å2 / Biso mean: 18.5688 Å2 / Biso min: 8.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.41→45.926 Å
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Refine LS restraints |
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LS refinement shell |
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