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Yorodumi- PDB-141l: ROLE OF BACKBONE FLEXIBILITY IN THE ACCOMMODATION OF VARIANTS THA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 141l | ||||||
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Title | ROLE OF BACKBONE FLEXIBILITY IN THE ACCOMMODATION OF VARIANTS THAT REPACK THE CORE OF T4 LYSOZYME | ||||||
Components | T4 LYSOZYME | ||||||
Keywords | HYDROLASE(O-GLYCOSYL) | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Baldwin, E. / Matthews, B.W. | ||||||
Citation | Journal: Science / Year: 1993 Title: The role of backbone flexibility in the accommodation of variants that repack the core of T4 lysozyme. Authors: Baldwin, E.P. / Hajiseyedjavadi, O. / Baase, W.A. / Matthews, B.W. #1: Journal: Techniques in Protein Chemistry Iv / Year: 1993 Title: Construction and Functional Selection of a T4 Lysozyme Gene Library Randomly Mutagenized at Five Specific Sites Authors: Baldwin, E. / Xu, J. / Hajiseyedjavadi, O. #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 Angstroms Resolution Authors: Weaver, L.H. / 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 THE 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 141l.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb141l.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 141l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 141l_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 141l_full_validation.pdf.gz | 425.8 KB | Display | |
Data in XML | 141l_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 141l_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/41/141l ftp://data.pdbj.org/pub/pdb/validation_reports/41/141l | HTTPS FTP |
-Related structure data
Related structure data | 140lC 142lC 143lC 144lC 145lC 146lC 147lC C: citing same article (ref.) |
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Similar structure data |
-Links
-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. |
-Components
#1: Protein | Mass: 18660.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.89 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.7 / Method: batch method / Details: Remington, S.J., (1978) J. Mol. Biol., 118, 81. | ||||||||||||||||||||||||||||||||||||||||||||||||
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 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.153 / Highest resolution: 2 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. ...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. MUTANT SPACE GROUP, P3(2)21, IS ISOMORPHOUS TO WILD TYPE. STARTING COORDINATES WERE BASED ON THE CYS-FREE WILD-TYPE MODEL. | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Rfactor obs: 0.153 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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