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Yorodumi- PDB-229l: GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 229l | ||||||
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Title | GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS | ||||||
Components | T4 LYSOZYME | ||||||
Keywords | HYDROLASE / O-GLYCOSYL / T4 LYSOZYME / CAVITY MUTANTS / LIGAND BINDING / PROTEIN ENGINEERING / PROTEIN DESIGN | ||||||
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: 1.8 Å | ||||||
Authors | Baldwin, E.P. / Baase, W.A. / Zhang, X.-J. / Feher, V. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions. Authors: Baldwin, E. / Baase, W.A. / Zhang, X. / Feher, V. / Matthews, B.W. #1: Journal: Nature / Year: 1992 Title: A Cavity-Containing Mutant of T4 Lysozyme is Stabilized by Buried Benzene Authors: Eriksson, A.E. / Baase, W.A. / Wozniak, J.A. / Matthews, B.W. #2: Journal: Methods Enzymol. / Year: 1989 Title: Expression and Nitrogen-15 Labeling of Proteins for Proton and Nitrogen-15 Nuclear Magnetic Resonance Authors: Muchmore, D.C. / Mcintosh, L.P. / Russell, C.B. / Anderson, D.E. / Dahlquist, F.W. #3: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 A Resolution Authors: Weaver, L.H. / 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 | 229l.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb229l.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 229l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 229l_validation.pdf.gz | 435 KB | Display | wwPDB validaton report |
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Full document | 229l_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 229l_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 229l_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/29/229l ftp://data.pdbj.org/pub/pdb/validation_reports/29/229l | HTTPS FTP |
-Related structure data
Related structure data | 220lC 222lC 223lC 225lC 226lC 227lC 228lC 252lC C: citing same article (ref.) |
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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
#1: Protein | Mass: 18542.246 Da / Num. of mol.: 1 / Mutation: C54T, R95A, C97A Source method: isolated from a genetically manipulated source Details: GUANIDINIUM LIGAND / Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Cellular location: CYTOPLASM / Gene: GENE E / Plasmid: PHS1403 / 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-GAI / | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | STRUCTURE OF A T4 LYSOZYME MUTANT WITH A POLAR CREVICE, CREATED BY TRUNCATING ARG 95 TO ALA. ARG 95 ...STRUCTURE OF A T4 LYSOZYME MUTANT WITH A POLAR CREVICE, CREATED BY TRUNCATING | |
-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: 55.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 25 MM HEPES PH 7.5 WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 0.1 M NACL, 0.1 M KPO4,20% W/V ...Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 25 MM HEPES PH 7.5 WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 0.1 M NACL, 0.1 M KPO4,20% W/V PEG 3350,PH 7.1, 0.25 M GUAD-HCL (LIGAND)., pH 7.0, vapor diffusion - hanging drop, temperature 277K PH range: 7.1-7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Remington, S.J., (1978). J. Mol. Biol., 118, 81. / pH: 6.7 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: Jul 20, 1993 / Details: GRAPHITE MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 18659 / % possible obs: 92 % / Rmerge(I) obs: 0.033 |
Reflection shell | Highest resolution: 1.8 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: CYS-FREE WILD TYPE LYSOZYME Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 132 Å2 / ksol: 0.46 e/Å3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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