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- PDB-129l: STRUCTURES OF RANDOMLY GENERATED MUTANTS OF T4 LYSOZYME SHOW THAT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 129l | ||||||
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Title | STRUCTURES OF RANDOMLY GENERATED MUTANTS OF T4 LYSOZYME SHOW THAT PROTEIN STABILITY CAN BE ENHANCED BY RELAXATION OF STRAIN AND BY IMPROVED HYDROGEN BONDING VIA BOUND SOLVENT | ||||||
![]() | T4 LYSOZYME | ||||||
![]() | HYDROLASE(O-GLYCOSYL) | ||||||
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 | ![]() | ||||||
![]() | Pjura, P. / Matthews, B.W. | ||||||
![]() | ![]() Title: Structures of randomly generated mutants of T4 lysozyme show that protein stability can be enhanced by relaxation of strain and by improved hydrogen bonding via bound solvent. Authors: Pjura, P. / Matthews, B.W. #1: ![]() Title: Development of an in Vivo Method to Identify Mutants of Phage T4 Lysozyme of Enhanced Thermostability Authors: Pjura, P. / Matsumura, M. / Baase, W.A. / Matthews, B.W. | ||||||
History |
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Remark 700 | SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT ...SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT CONVENIENTLY BE REPRESENTED IN HELIX AND SHEET RECORDS BELOW. THESE ASPECTS INFLUENCE THE REPRESENTATION OF HELIX 6 AND STRAND 3 OF SHEET *S1*. THE PAPER J.MOL.BIOL., V. 118, P. 81, 1978 SHOULD BE CONSULTED FOR THESE SUBTLETIES. |
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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 | ![]() | 34.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS ENTRY DOES NOT INCLUDE RESIDUES 163 AND 164. 2: SEO 901 FORMS AN S-S LINKAGE TO SEO 902. |
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Components
#1: Protein | Mass: 18658.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.94 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 5 ℃ / Method: unknown / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. all: 49980 / Num. obs: 17845 / Rmerge(I) obs: 0.048 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.165 / Highest resolution: 1.7 Å Details: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS ENTRY DOES NOT INCLUDE RESIDUES 163 AND 164. | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 17806 / Rfactor obs: 0.165 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d / Dev ideal: 2.7 |