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Yorodumi- PDB-212l: PROTEIN STRUCTURE PLASTICITY EXEMPLIFIED BY INSERTION AND DELETIO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 212l | ||||||
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Title | PROTEIN STRUCTURE PLASTICITY EXEMPLIFIED BY INSERTION AND DELETION MUTANTS IN T4 LYSOZYME | ||||||
Components | T4 LYSOZYME | ||||||
Keywords | HYDROLASE (O-GLYCOSYL) / 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: 1.76 Å | ||||||
Authors | Vetter, I.R. / Baase, W.A. / Heinz, D.W. / Xiong, J.-P. / Snow, S. / Matthews, B.W. | ||||||
Citation | Journal: Protein Sci. / Year: 1996 Title: Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme. Authors: Vetter, I.R. / Baase, W.A. / Heinz, D.W. / Xiong, J.P. / Snow, S. / Matthews, B.W. #1: Journal: Nature / Year: 1993 Title: How Amino-Acid Insertions are Allowed in an Alpha-Helix of T4 Lysozyme Authors: Heinz, D.W. / Baase, W.A. / Dahlquist, F.W. / 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 | 212l.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb212l.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 212l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 212l_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 212l_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 212l_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 212l_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/12/212l ftp://data.pdbj.org/pub/pdb/validation_reports/12/212l | HTTPS FTP |
-Related structure data
Related structure data | 209lC 210lC 211lC 213lC 214lC 215lC 218lC 219lC 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: 18912.678 Da / Num. of mol.: 1 / Mutation: C54T, C97A, INS(L164-AAAA) 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 | ChemComp-HED / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 48.3 % | ||||||||||||||||||||
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Crystal grow | Details: MUTANT CRYSTALLIZED FROM PEG IN CONTRAST TO L164AAAA WHICH WAS CRYSTALLIZED FROM PHOSPHATE. | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Nov 2, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→35.65 Å / Num. obs: 20392 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.0622 |
-Processing
Software |
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Refinement | Resolution: 1.76→35.65 Å / σ(F): 0 Details: RESIDUES 162 - 168 IN THIS MUTANT LYSOZYME ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS MUTANT WAS CRYSTALLIZED FROM PEG, AS COMPARED TO ENTRY 219L ...Details: RESIDUES 162 - 168 IN THIS MUTANT LYSOZYME ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS MUTANT WAS CRYSTALLIZED FROM PEG, AS COMPARED TO ENTRY 219L WHICH IS THE SAME MUTANT, BUT CRYSTALLIZED FROM PHOSPHATE.
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Refinement step | Cycle: LAST / Resolution: 1.76→35.65 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.156 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.019 / Weight: 3 |