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Open data
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Basic information
Entry | Database: PDB / ID: 260l | ||||||
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Title | AN ADAPTABLE METAL-BINDING SITE ENGINEERED INTO T4 LYSOZYME | ||||||
![]() | PROTEIN (LYSOZYME) | ||||||
![]() | HYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / METAL BINDING / PROTEIN ENGINEERING / PROTEIN DESIGN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wray, J.W. / Baase, W.A. / Ostheimer, G.J. / Matthews, B.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() Title: Control of Enzyme Activity by an Engineered Disulfide Bond Authors: Matsumura, M. / Matthews, B.W. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.6 KB | Display | ![]() |
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PDB format | ![]() | 33.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.8 KB | Display | ![]() |
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Full document | ![]() | 422 KB | Display | |
Data in XML | ![]() | 9.6 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() 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: ![]() ![]() | ||||||||||
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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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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