+Open data
-Basic information
Entry | Database: PDB / ID: 1c6p | ||||||
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Title | T4 LYSOZYME MUTANT C54T/C97A IN THE PRESENCE OF 8 ATM ARGON | ||||||
Components | PROTEIN (LYSOZYME) | ||||||
Keywords | HYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / NOBLE GAS BINDING | ||||||
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: 1.9 Å | ||||||
Authors | Quillin, M.L. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Size versus polarizability in protein-ligand interactions: binding of noble gases within engineered cavities in phage T4 lysozyme. Authors: Quillin, M.L. / Breyer, W.A. / Griswold, I.J. / Matthews, B.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989 Title: Stabilization of Phage T4 Lysozyme by Engineered Disulfide Bonds Authors: Matsumura, M. / Becktel, W.J. / Levitt, M. / 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 | 1c6p.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c6p.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/1c6p ftp://data.pdbj.org/pub/pdb/validation_reports/c6/1c6p | HTTPS FTP |
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-Related structure data
Related structure data | 1c60C 1c61C 1c62C 1c63C 1c64C 1c65C 1c66C 1c67C 1c68C 1c69C 1c6aC 1c6bC 1c6cC 1c6dC 1c6eC 1c6fC 1c6gC 1c6hC 1c6iC 1c6jC 1c6kC 1c6lC 1c6mC 1c6nC 1c6qC 1c6tC 1l63S S: Starting model for refinement 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: 18628.363 Da / Num. of mol.: 1 / Mutation: YES 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: GENE E / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Details: 1.8-2.2 M NAH2/K2HPO4, PH 6.9-7.1, 50 MM BETA-MERCAPTOETHANOL AND/OR 50 MM HYDROXYETHYL DISULFIDE PH range: 6.9-7 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 11, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→60 Å / Num. obs: 15469 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 2.67 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.22 / % possible all: 99 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Starting model: 1L63 Resolution: 1.9→60 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: MOEWS AND KRETSINGER / Bsol: 300.2 Å2 / ksol: 0.947 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→60 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.015 / Weight: 5 |