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Yorodumi- PDB-1lyd: CRYSTAL STRUCTURE OF T4-LYSOZYME GENERATED FROM SYNTHETIC CODING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lyd | ||||||
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Title | CRYSTAL STRUCTURE OF T4-LYSOZYME GENERATED FROM SYNTHETIC CODING DNA EXPRESSED IN ESCHERICHIA COLI | ||||||
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 | Rose, D.R. | ||||||
Citation | Journal: Protein Eng. / Year: 1988 Title: Crystal structure of T4-lysozyme generated from synthetic coding DNA expressed in Escherichia coli. Authors: Rose, D.R. / Phipps, J. / Michniewicz, J. / Birnbaum, G.I. / Ahmed, F.R. / Muir, A. / Anderson, W.F. / Narang, S. #1: Journal: Protein Eng. / Year: 1987 Title: Hierarchical Strategy for Protein Folding and Design. Synthesis and Expression of T4 Lysozyme Gene and Two Putative Folding Mutants Authors: Narang, S.A. / Yao, F.-L. / Michniewicz, J.J. / Dubuc, G. / Phipps, J. / Somorjai, R.L. #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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lyd.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lyd.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1lyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1lyd ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1lyd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 WERE NOT VISIBLE ON THE ELECTRON DENSITY MAP. THEIR POSITIONS ARE UNCERTAIN. |
-Components
#1: Protein | Mass: 18662.467 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 |
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#2: Water | ChemComp-HOH / |
Compound details | THE SECONDARY STRUCTURE PRESENTED IN THIS ENTRY IS THE SAME AS THAT IN PROTEIN DATA BANK ENTRY 2LZM. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.83 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.7 / Method: vapor diffusion, hanging drop | |||||||||||||||
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 / Lowest resolution: 1.9 Å / Num. obs: 19039 / % possible obs: 89 % / Num. measured all: 58869 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å Details: RESIDUES 162 - 164 WERE NOT VISIBLE ON THE ELECTRON DENSITY MAP. THEIR POSITIONS ARE UNCERTAIN
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 9177 / σ(F): 3 / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15 Å2 |