+Open data
-Basic information
Entry | Database: PDB / ID: 260l | ||||||
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Title | AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME | ||||||
Components | PROTEIN (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. / 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 Angstrom 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 | 260l.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb260l.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 260l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/60/260l ftp://data.pdbj.org/pub/pdb/validation_reports/60/260l | 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: C54T,C97A,T21H,T142H Source method: isolated from a genetically manipulated source Details: T4 LYSOZYME MUTANT WITH CYS 54 REPLACED BY THR, CYS 97 REPLACED BY ALA, THR 21 REPLACED BY HIS, THR 142 REPLACED BY HIS Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato Description: BACTERIOPHAGE T4 (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 | #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 | Nonpolymer details | NICKEL 2+ IS BOUND TO THE ENGINEERED PROTEIN LIGANDS HIS 21 AND HIS 142, WITH HOH 501-504 AS THE ...NICKEL 2+ IS BOUND TO THE ENGINEERED | Sequence details | RESIDUES 163 AND 164 ARE DISORDERED AND NOT OBSERVABLE IN ELECTRON DENSITY MAPS. THEREFORE THEY ARE ...RESIDUES 163 AND 164 ARE DISORDERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.43 % / Description: STARTING MODEL WAS CYS-FREE WILDTYPE LYSOZYME | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jan 19, 1998 / Details: GRAPHITE MONOCHROMATOR |
Radiation | Monochromator: NI FILTER/GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 19963 / % possible obs: 92 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.031 |
Reflection shell | Highest resolution: 1.8 Å / Rmerge(I) obs: 0.18 / 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: 790 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 σ(F): 0 / Rfactor all: 0.19 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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