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Yorodumi- PDB-1l16: STRUCTURAL ANALYSIS OF THE TEMPERATURE-SENSITIVE MUTANT OF BACTER... -
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-Basic information
Entry | Database: PDB / ID: 1l16 | |||||||||
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Title | STRUCTURAL ANALYSIS OF THE TEMPERATURE-SENSITIVE MUTANT OF BACTERIOPHAGE T4 LYSOZYME, GLYCINE 156 (RIGHT ARROW) ASPARTIC ACID | |||||||||
Components | T4 LYSOZYME | |||||||||
Keywords | HYDROLASE (O-GLYCOSYL) | |||||||||
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 / Resolution: 1.7 Å | |||||||||
Authors | Gray, T.M. / Matthews, B.W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1987 Title: Structural analysis of the temperature-sensitive mutant of bacteriophage T4 lysozyme, glycine 156----aspartic acid. Authors: Gray, T.M. / Matthews, B.W. #1: Journal: Nature / Year: 1987 Title: Contributions of Hydrogen Bonds of Thr 157 to the Thermodynamic Stability of Phage T4 Lysozyme Authors: Alber, T. / Dao-Pin, S. / Wilson, K. / Wozniak, J.A. / Cook, S.P. / Matthews, B.W. #2: Journal: J.Mol.Biol. / Year: 1987 Title: Structural Studies of Mutants of the Lysozyme of Bacteriophage T4. The Temperature-Sensitive Mutant Protein Thr157 (Right Arrow) Ile Authors: Gruetter, M.G. / Gray, T.M. / Weaver, L.H. / Alber, T. / Wilson, K. / Matthews, B.W. #3: Journal: J.Mol.Biol. / Year: 1987 Title: Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution Authors: Weaver, L.H. / Matthews, B.W. #4: Journal: Biochemistry / Year: 1987 Title: Temperature-Sensitive Mutations of Bacteriophage T4 Lysozyme Occur at Sites with Low Mobility and Low Solvent Accessibility in the Folded Protein Authors: Alber, T. / Dao-Pin, S. / Nye, J.A. / Muchmore, D.C. / Matthews, B.W. #5: Journal: Nature / Year: 1981 Title: Common Precursor of Lysozymes of Hen Egg-White and Bacteriophage T4 Authors: Matthews, B.W. / Gruetter, M.G. / Anderson, W.F. / Remington, S.J. #6: Journal: J.Mol.Biol. / Year: 1981 Title: Crystallographic Determination of the Mode of Binding of Oligosaccharides to T4 Bacteriophage Lysozyme. Implications for the Mechanism of Catalysis Authors: Anderson, W.F. / Gruetter, M.G. / Remington, S.J. / Weaver, L.H. / Matthews, B.W. #7: Journal: J.Mol.Biol. / Year: 1981 Title: Relation between Hen Egg White Lysozyme and Bacteriophage T4 Lysozyme. Evolutionary Implications Authors: Matthews, B.W. / Remington, S.J. / Gruetter, M.G. / Anderson, W.F. #8: Journal: J.Mol.Biol. / Year: 1978 Title: Structure of the Lysozyme from Bacteriophage T4, an Electron Density Map at 2.4 Angstroms Resolution Authors: Remington, S.J. / Anderson, W.F. / Owen, J. / Teneyck, L.F. / Grainger, C.T. / Matthews, B.W. #9: Journal: Biochem.Biophys.Res.Commun. / Year: 1977 Title: Atomic Coordinates for T4 Phage Lysozyme Authors: Remington, S.J. / Teneyck, L.F. / Matthews, B.W. #10: Journal: Biochim.Biophys.Acta / Year: 1975 Title: Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme Authors: Matthews, B.W. #11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1974 Title: The Three Dimensional Structure of the Lysozyme from Bacteriophage T4 Authors: Matthews, B.W. / Remington, S.J. #12: Journal: J.Mol.Biol. / Year: 1973 Title: Crystallographic Data for Lysozyme from Bacteriophage T4 Authors: Matthews, B.W. / Dahlquist, F.W. / Maynard, A.Y. | |||||||||
History |
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Remark 700 | SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT ...SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT CONVENIENTLY BE REPRESENTED IN THE HELIX AND SHEET RECORDS BELOW. THESE ASPECTS INFLUENCE THE REPRESENTATION OF HELIX 6 AND STRAND 3 OF SHEET *S1*. THE PAPER CITED IN REFERENCE 8 ABOVE SHOULD BE CONSULTED FOR THESE SUBTLETIES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l16.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l16.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 1l16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l16_validation.pdf.gz | 418.2 KB | Display | wwPDB validaton report |
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Full document | 1l16_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 1l16_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1l16_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/1l16 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/1l16 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 18720.504 Da / Num. of mol.: 1 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 / Plasmid: M13 / References: UniProt: P00720, lysozyme |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.7 / Method: batch methodDetails: taken from Remington, S.J. et al (1978). J. Mol. Biol., 81-98. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient pressure: 101 kPa / Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Target: Cu / Voltage: 40 kV |
Detector | Type: OSCILLATION CAMERA / Detector: FILM / Details: Kodak No-Screen X-ray film |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å |
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 15606 / Rmerge(I) obs: 0.052 |
-Processing
Software |
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Refinement | Resolution: 1.7→6 Å / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.177 / Highest resolution: 1.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 15606 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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