+Open data
-Basic information
Entry | Database: PDB / ID: 255l | |||||||||
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Title | HYDROLASE | |||||||||
Components | LYSOZYME | |||||||||
Keywords | HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME | |||||||||
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: 1.8 Å | |||||||||
Authors | Kuroki, R. / Shoichet, B. / Weaver, L.H. / Matthews, B.W. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1995 Title: A relationship between protein stability and protein function. Authors: Shoichet, B.K. / Baase, W.A. / Kuroki, R. / Matthews, B.W. #1: Journal: Science / Year: 1993 Title: A Covalent Enzyme-Substrate Intermediate with Saccharide Distortion in a Mutant T4 Lysozyme Authors: Kuroki, R. / Weaver, L.H. / Matthews, B.W. #2: 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 | 255l.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb255l.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 255l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 255l_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 255l_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 255l_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 255l_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/55/255l ftp://data.pdbj.org/pub/pdb/validation_reports/55/255l | HTTPS FTP |
-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: 18627.377 Da / Num. of mol.: 1 / Mutation: D20N, C54T, C97A 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 / Gene: T4 LYSOZYME GENE / Plasmid: M13 / Gene (production host): T4 LYSOZYME GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | #3: Chemical | ChemComp-BME / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.7 / Method: batch method / Details: Weaver, L.H., (1987) J. Mol. Biol., 193, 189. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.709→30 Å / Num. obs: 19526 / Rmerge(I) obs: 0.0314 / Net I/σ(I): 11.83 |
Reflection | *PLUS |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→30 Å
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Solvent computation | Bsol: 418 Å2 / ksol: 1.05 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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