+Open data
-Basic information
Entry | Database: PDB / ID: 258l | ||||||
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Title | AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / METAL BINDING / PROTEIN ENGINEERING / PROTEIN DESIGN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wray, J.W. / Baase, W.A. / Ostheimer, G.J. / Matthews, B.W. | ||||||
Citation | Journal: Protein Eng. / Year: 2000 Title: Use of a non-rigid region in T4 lysozyme to design an adaptable metal-binding site. Authors: Wray, J.W. / Baase, W.A. / Ostheimer, G.J. / Zhang, X.J. / Matthews, B.W. #1: 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. #2: Journal: Science / Year: 1989 Title: Control of Enzyme Activity by an Engineered Disulfide Bond Authors: Matsumura, M. / Matthews, B.W. #3: 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 | 258l.cif.gz | 48.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb258l.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 258l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/58/258l ftp://data.pdbj.org/pub/pdb/validation_reports/58/258l | HTTPS FTP |
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-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: 18702.449 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 Description: MUTANT GENE DERIVED FROM THE M13 PLASMID BY CLONING THE T4 LYSOZYME GENE Cellular location: CYTOPLASM / Gene: GENE E FROM BACTERIOPHAGE T4 / Plasmid: PHS1403 / Gene (production host): T4 LYSOZYME / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Compound details | STRUCTURE OF A T4 LYSOZYME MUTANT WITH AN ENGINEERED METAL BINDING SITE. THIS MUTANT DESIGNATED ...STRUCTURE OF A T4 LYSOZYME MUTANT WITH AN ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.52 % / Description: STARTING MODEL WAS CYS-FREE WILDTYPE LYSOZYME | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 9, 1997 / Details: GRAPHITE MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 17343 / % possible obs: 82 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.032 |
Reflection shell | Highest resolution: 1.8 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Redundancy: 2.5 % |
Reflection shell | *PLUS Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO / Details: STARTING MODEL WAS CYS-FREE WILDTYPE
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Solvent computation | Solvent model: BABENET SCALING / Bsol: 695 Å2 / ksol: 1 e/Å3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.173 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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