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Yorodumi- PDB-125l: THE ENERGETIC COST AND THE STRUCTURAL CONSEQUENCES OF BURYING A H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 125l | ||||||
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Title | THE ENERGETIC COST AND THE STRUCTURAL CONSEQUENCES OF BURYING A HYDROXYL GROUP WITHIN THE CORE OF A PROTEIN DETERMINED FROM ALA TO SER AND VAL TO THR SUBSTITUTIONS IN 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: 1.85 Å | ||||||
Authors | Blaber, M. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. Authors: Blaber, M. / Lindstrom, J.D. / Gassner, N. / Xu, J. / Heinz, D.W. / Matthews, B.W. #1: Journal: Science / Year: 1989 Title: Control of Enzyme Activity by an Engineered Disulfide Bond Authors: Matsumura, M. / Matthews, B.W. #2: 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 | 125l.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb125l.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 125l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 125l_validation.pdf.gz | 416.3 KB | Display | wwPDB validaton report |
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Full document | 125l_full_validation.pdf.gz | 419.5 KB | Display | |
Data in XML | 125l_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 125l_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/25/125l ftp://data.pdbj.org/pub/pdb/validation_reports/25/125l | HTTPS FTP |
-Related structure data
Related structure data | 118lC 119lC 120lC 122lC 123lC 126lC 127lC 128lC 206lC 221lC 224lC 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: 18644.363 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 / Plasmid: M13 / 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: 2.78 Å3/Da / Density % sol: 55.78 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.9 / Method: batch method / Details: Matthew, B.W., (1973) J. Mol. Biol., 78, 575. / PH range low: 7.3 / PH range high: 6.7 | ||||||||||||||||||||||||||||||||||||
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: 1.85 Å / Num. obs: 15492 / % possible obs: 82 % / Rmerge(I) obs: 0.024 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.144 / Highest resolution: 1.85 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: 1.85 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.85 Å / Rfactor obs: 0.144 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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