+Open data
-Basic information
Entry | Database: PDB / ID: 5jwu | ||||||
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Title | T4 Lysozyme L99A/M102Q with 1,2-Dihydro-1,2-azaborine 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 sensu lato (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 5jwu.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jwu.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 5jwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/5jwu ftp://data.pdbj.org/pub/pdb/validation_reports/jw/5jwu | HTTPS FTP |
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-Related structure data
Related structure data | 5jwsC 5jwtC 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 on special symmetry positions |
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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 sensu lato (virus) Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||
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#2: Chemical | ChemComp-B20 / | ||
#3: Chemical | #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: 277.15 K / Method: vapor diffusion, hanging drop Details: 2.1 M sodium/potassium phosphate, pH 7.0, 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: 1.7→45.84 Å / Num. obs: 22416 / % possible obs: 98.1 % / Redundancy: 8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.438 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LGU Resolution: 1.7→45.84 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.62 Å2 / Biso mean: 29.85 Å2 / Biso min: 17.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→45.84 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: 8
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