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- PDB-1dyb: DETERMINATION OF ALPHA-HELIX PROPENSITY WITHIN THE CONTEXT OF A F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dyb | ||||||
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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 | ||||||
![]() | 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 | ![]() | ||||||
![]() | Zhang, X. / Matthews, B.W. | ||||||
![]() | ![]() 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: ![]() Title: Structural Basis of Amino Acid Alpha-Helix Propensity Authors: Blaber, M. / Zhang, X.-J. / Matthews, B.W. #2: ![]() Title: Control of Enzyme Activity by an Engineered Disulfide Bond Authors: Matsumura, M. / Matthews, B.W. #3: ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.6 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 | ![]() 1dyaC ![]() 1dycC ![]() 1dydC ![]() 1dyeC ![]() 1dyfC ![]() 1dygC ![]() 3l64C 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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1 |
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Unit cell |
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Atom site foot note | 1: SG SEO 97 IS BONDED TO SG CYS 97. |
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Components
#1: Protein | Mass: 18620.387 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: 2.8 Å3/Da / Density % sol: 56.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 1.75 Å / Num. obs: 13956 / % possible obs: 68 % / Rmerge(I) obs: 0.148 |
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Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.75→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: 1.75→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 6 Å / Num. reflection all: 13956 / σ(F): 0 / Rfactor all: 0.173 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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