+Open data
-Basic information
Entry | Database: PDB / ID: 234l | ||||||
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Title | T4 LYSOZYME MUTANT M106L | ||||||
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. / Drew, D.L. / Gassner, N. / 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 | 234l.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb234l.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 234l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/34/234l ftp://data.pdbj.org/pub/pdb/validation_reports/34/234l | 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: C54T, C97A, M106L 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 218, 198, 522, 540, 216, 249, 500, 502, AND 564 HAVE CLOSE CONTACTS AND MAY BE ...SOLVENT MOLECULES 218, 198, 522, 540, 216, 249, 500, 502, AND 564 HAVE CLOSE CONTACTS AND MAY BE PARTIALLY OCCUPIED METAL IONS (PROBABLY SODIUM OR POTASSIUM). | |
-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: 55.97 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||
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: Apr 1, 1997 / 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: 1.88→30 Å / Num. obs: 15629 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.88→1.98 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 2.5 / % possible all: 53.4 |
Reflection shell | *PLUS % possible obs: 53.4 % |
-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: 730 Å2 / ksol: 1.141 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: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.012 / Weight: 5 |