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Yorodumi- PDB-1dyc: DETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dyc | ||||||
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Title | DETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A FOLDED PROTEIN: SITES 44 AND 131 IN BACTERIOPHAGE 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: 2.1 Å | ||||||
Authors | Zhang, X. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Determination of alpha-helix propensity within the context of a folded protein. Sites 44 and 131 in bacteriophage T4 lysozyme. Authors: Blaber, M. / Zhang, X.J. / Lindstrom, J.D. / Pepiot, S.D. / Baase, W.A. / Matthews, B.W. #1: Journal: To be Published Title: Structural Basis of Amino Acid Alpha-Helix Propensity Authors: Blaber, M. / Zhang, X.-J. / Matthews, B.W. #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 | 1dyc.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dyc.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dyc_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 1dyc_full_validation.pdf.gz | 434 KB | Display | |
Data in XML | 1dyc_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1dyc_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyc ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyc | HTTPS FTP |
-Related structure data
Related structure data | 1dyaC 1dybC 1dydC 1dyeC 1dyfC 1dygC 3l64C 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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-Components
#1: Protein | Mass: 18676.494 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 | ChemComp-BME / | #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: 55.91 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.7 / Method: batch methodDetails: referred to 'Remington, S. J.', (1978) J. Mol. Biol., 118, 81-98 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.1 Å / Num. obs: 9388 / % possible obs: 79 % / Rmerge(I) obs: 0.121 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→6 Å / σ(F): 0 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.
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Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 6 Å / Num. reflection all: 9388 / σ(F): 0 / Rfactor all: 0.152 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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