[English] 日本語
Yorodumi- PDB-152l: CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF T4 L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 152l | ||||||
---|---|---|---|---|---|---|---|
Title | CONSERVATION OF SOLVENT-BINDING SITES IN 10 CRYSTAL FORMS OF T4 LYSOZYME | ||||||
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: 2 Å | ||||||
Authors | Matsumura, M. / Weaver, L.H. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme. Authors: Zhang, X.J. / Matthews, B.W. #1: Journal: To be Published Title: A Covalent Enzyme-Substrate Intermediate with Saccharide Distorsion in a Mutant T4 Lysozyme Authors: Kuroki, R. / Weaver, L.H. / Matthews, B.W. #2: Journal: Protein Sci. / Year: 1992 Title: Structure of a Stabilizing Disulfide Bridge Mutant that Closes the Active-Site Cleft of T4 Lysozyme Authors: Jacobson, R.H. / Matsumura, M. / Faber, H.R. / Matthews, B.W. #3: Journal: Biochemistry / Year: 1990 Title: Structure of a Thermostable Disulfide-Bridge Mutant of Phage T4 Lysozyme Shows that an Engineered Cross-Link in a Flexible Region Does not Increase the Rigidity of the Folded Protein Authors: Pjura, P.E. / Matsumura, M. / Wozniak, J.A. / Matthews, B.W. #4: Journal: Nature / Year: 1989 Title: Substantial Increase of Protein Stability by Multiple Disulphide Bonds Authors: Matsumura, M. / Signor, G. / Matthews, B.W. #5: 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 152l.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb152l.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 152l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/52/152l ftp://data.pdbj.org/pub/pdb/validation_reports/52/152l | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18634.461 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 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.98 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 8.5 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Ambient pressure: 101 kPa / Mean temperature: 298 K |
---|---|
Diffraction source | Source: rotating-anode X-ray tube / Type: RIGAKU RU200 / Target: Cu |
Detector | Type: AREA DETECTOR / Detector: AREA DETECTOR / Details: Xuong-Hamlin |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å |
Radiation wavelength | Relative weight: 1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→50 Å / Rfactor obs: 0.168 / σ(F): 0 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor all: 0.168 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|