+Open data
-Basic information
Entry | Database: PDB / ID: 230l | ||||||
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Title | T4 LYSOZYME MUTANT M6L | ||||||
Components | T4 LYSOZYME | ||||||
Keywords | HYDROLASE / O-GLYCOSYL / GLYCOSIDASE | ||||||
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 / DIFFERENCE FOURIER / Resolution: 1.9 Å | ||||||
Authors | Lipscomb, L.A. / Gassner, N.C. / Snow, S. / Eldridge, A.M. / Drew, D.L. / Baase, W.A. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Context-dependent protein stabilization by methionine-to-leucine substitution shown in T4 lysozyme. Authors: Lipscomb, L.A. / Gassner, N.C. / Snow, S.D. / Eldridge, A.M. / Baase, W.A. / Drew, D.L. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 230l.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb230l.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 230l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/30/230l ftp://data.pdbj.org/pub/pdb/validation_reports/30/230l | 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: 18610.324 Da / Num. of mol.: 1 / Mutation: M6L, C54T, C97A 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 Description: MUTANT GENE DERIVED FROM THE M13 PLASMID BY CLONING THE T4 LYSOZYME GENE Cell line: S2 / Cellular location: CYTOPLASM / Gene: T4 LYSOZYME / Plasmid: M13 / Gene (production host): T4 LYSOZYME / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BME / | #4: Water | ChemComp-HOH / | Nonpolymer details | SOLVENT MOLECULES 227, 236, 250, 251, 256, 281, 357, 358, AND 372 APPEAR TO HAVE CLOSE CONTACTS AND ...SOLVENT MOLECULES 227, 236, 250, 251, 256, 281, 357, 358, AND 372 APPEAR TO HAVE CLOSE CONTACTS AND ARE PROBABLY PARTIALLY OCCUPIED WATER MOLECULES OR METAL (SODIUM OR POTASSIUM) IONS. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.96 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: M6L WAS AT 15MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL. IT WAS DILUTED BY 1/2 WITH A SOLUTION 1.8M IN NA/KPO4 PH 6.9. THIS WAS ALSO THE WELL SOLUTION. HANGING DROP METHODS ...Details: M6L WAS AT 15MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL. IT WAS DILUTED BY 1/2 WITH A SOLUTION 1.8M IN NA/KPO4 PH 6.9. THIS WAS ALSO THE WELL SOLUTION. HANGING DROP METHODS WERE USED., pH 7.0, vapor diffusion - hanging drop PH range: 6.6-6.9 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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 RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jan 1, 1996 / Details: GRAPHITE MONOCHROMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 16280 / % possible obs: 77 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.76→1.9 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 1.9 / % possible all: 45.6 |
Reflection shell | *PLUS % possible obs: 45.6 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 1.9→30 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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