+Open data
-Basic information
Entry | Database: PDB / ID: 231l | ||||||
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Title | T4 LYSOZYME MUTANT M106K | ||||||
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: 2.5 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 | 231l.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb231l.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 231l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/31/231l ftp://data.pdbj.org/pub/pdb/validation_reports/31/231l | 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: 18626.348 Da / Num. of mol.: 1 / Mutation: C54T, C97A, M106K 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 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 | ChemComp-CL / |
#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: 2.79 Å3/Da / Density % sol: 55.97 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: M106K WAS AT 19MG/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 ...Details: M106K WAS AT 19MG/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: 6.9 / 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, 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: 2.5→30 Å / Num. obs: 10567 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.37→2.61 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 1.6 / % possible all: 93.9 |
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.5→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: 2.5→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: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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