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- PDB-225l: 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: 225l | ||||||
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Title | GENERATING LIGAND BINDING SITES IN T4 LYSOZYME USING DEFICIENCY-CREATING SUBSTITUTIONS | ||||||
![]() | T4 LYSOZYME | ||||||
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Function / homology | ![]() viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / ![]() ![]() 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 | ![]() | 49 KB | Display | ![]() |
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PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 220lC ![]() 222lC ![]() 223lC ![]() 226lC ![]() 227lC ![]() 228lC ![]() 229lC ![]() 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: 18606.359 Da / Num. of mol.: 1 / Mutation: L133G Source method: isolated from a genetically manipulated source Details: P-XYLENE LIGANDED / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-PXY / ![]() | ||||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Compound details | STRUCTURE OF A HYDROPHOBI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 0.1M NA2PO4 PH 6.6, 0.55 M NACL WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 1.8-2.2M NA/KPO4 PH ...Details: CRYSTALS GROWN IN HANGING DROPS AT 4 DEGREES C. PROTEIN 10-20 MG/ML IN A BUFFER CONTAINING 0.1M NA2PO4 PH 6.6, 0.55 M NACL WAS DILUTED 1/2 WITH A WELL SOLUTION CONTAINING 1.8-2.2M NA/KPO4 PH 6.3-7.1 WITH OXIDIZED/REDUCED BME. CRYSTALS WERE EXPOSED TO P-XYLENE VAPOR IN A CAPILLARY FOR SEVERAL DAYS AT ROOM TEMPERATURE., pH 7.0, vapor diffusion - hanging drop, temperature 277K PH range: 6.3-7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: Sep 28, 1991 / Details: GRAPHITE MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→20 Å / % possible obs: 83 % / Rmerge(I) obs: 0.038 |
Reflection shell | Highest resolution: 1.9 Å / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure![]() Starting model: WILD TYPE T4 LYSOZYME Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 374 Å2 / ksol: 0.94 e/Å3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all![]() ![]() | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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