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- PDB-229l: GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 229l | ||||||
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Title | GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS | ||||||
![]() | T4 LYSOZYME | ||||||
![]() | HYDROLASE / O-GLYCOSYL / T4 LYSOZYME / CAVITY MUTANTS / LIGAND 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 | ![]() | ||||||
![]() | Baldwin, E.P. / Baase, W.A. / Zhang, X.-J. / Feher, V. / Matthews, B.W. | ||||||
![]() | ![]() Title: Generation of ligand binding sites in T4 lysozyme by deficiency-creating substitutions. Authors: Baldwin, E. / Baase, W.A. / Zhang, X. / Feher, V. / Matthews, B.W. #1: ![]() Title: A Cavity-Containing Mutant of T4 Lysozyme is Stabilized by Buried Benzene Authors: Eriksson, A.E. / Baase, W.A. / Wozniak, J.A. / Matthews, B.W. #2: ![]() Title: Expression and Nitrogen-15 Labeling of Proteins for Proton and Nitrogen-15 Nuclear Magnetic Resonance Authors: Muchmore, D.C. / Mcintosh, L.P. / Russell, C.B. / Anderson, D.E. / Dahlquist, F.W. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.8 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 439.2 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 220lC ![]() 222lC ![]() 223lC ![]() 225lC ![]() 226lC ![]() 227lC ![]() 228lC ![]() 252lC C: citing same article ( |
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Similar 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: 18542.246 Da / Num. of mol.: 1 / Mutation: C54T, R95A, C97A Source method: isolated from a genetically manipulated source Details: GUANIDINIUM LIGAND / Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-GAI / | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | STRUCTURE OF A T4 LYSOZYME MUTANT WITH A POLAR CREVICE, CREATED BY TRUNCATING ARG 95 TO ALA. ARG 95 ...STRUCTURE OF A T4 LYSOZYME MUTANT WITH A POLAR CREVICE, CREATED BY TRUNCATING | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 25 MM HEPES PH 7.5 WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 0.1 M NACL, 0.1 M KPO4,20% W/V ...Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 25 MM HEPES PH 7.5 WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 0.1 M NACL, 0.1 M KPO4,20% W/V PEG 3350,PH 7.1, 0.25 M GUAD-HCL (LIGAND)., pH 7.0, vapor diffusion - hanging drop, temperature 277K PH range: 7.1-7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Remington, S.J., (1978). J. Mol. Biol., 118, 81. / pH: 6.7 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 20, 1993 / Details: GRAPHITE MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 18659 / % possible obs: 92 % / Rmerge(I) obs: 0.033 |
Reflection shell | Highest resolution: 1.8 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: CYS-FREE WILD TYPE LYSOZYME Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 132 Å2 / ksol: 0.46 e/Å3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5F / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.16 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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