+Open data
-Basic information
Entry | Database: PDB / ID: 1lgu | ||||||
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Title | T4 Lysozyme Mutant L99A/M102Q | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Glycosidase / Bacteriolytic enzyme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wei, B.Q. / Baase, W.A. / Weaver, L.H. / Matthews, B.W. / Shoichet, B.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: A Model Binding Site for Testing Scoring Functions in Molecular Docking Authors: Wei, B.Q. / Baase, W.A. / Weaver, L.H. / Matthews, B.W. / 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 | 1lgu.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lgu.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/1lgu ftp://data.pdbj.org/pub/pdb/validation_reports/lg/1lgu | HTTPS FTP |
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-Related 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: 18617.320 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | #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: 2.78 Å3/Da / Density % sol: 55.75 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop / Details: Lipscomb, L.A., (1998) Protein Sci., 7, 765. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Mar 18, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. obs: 15427 / % possible obs: 88 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2393 / % possible all: 72 |
Reflection | *PLUS Lowest resolution: 15 Å / % possible obs: 88 % |
Reflection shell | *PLUS % possible obs: 72 % / Num. unique obs: 2393 / Rmerge(I) obs: 0.167 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: wild type T4 lysozyme Resolution: 1.9→15 Å / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: residues ASN163 and LEU164 are missing in the electron density
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |