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- PDB-1lyd: CRYSTAL STRUCTURE OF T4-LYSOZYME GENERATED FROM SYNTHETIC CODING ... -

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Basic information

Entry
Database: PDB / ID: 1lyd
TitleCRYSTAL STRUCTURE OF T4-LYSOZYME GENERATED FROM SYNTHETIC CODING DNA EXPRESSED IN ESCHERICHIA COLI
ComponentsT4 LYSOZYME
KeywordsHYDROLASE (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
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRose, 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
DepositionJan 11, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6621
Polymers18,6621
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.900, 60.900, 97.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUES 162 - 164 WERE NOT VISIBLE ON THE ELECTRON DENSITY MAP. THEIR POSITIONS ARE UNCERTAIN.

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Components

#1: Protein T4 LYSOZYME


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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SECONDARY STRUCTURE PRESENTED IN THIS ENTRY IS THE SAME AS THAT IN PROTEIN DATA BANK ENTRY 2LZM.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
11.41 M1reservoirNaH2PO4
21.15 M1reservoirK2HPO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.9 Å / Num. obs: 19039 / % possible obs: 89 % / Num. measured all: 58869

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→8 Å
Details: RESIDUES 162 - 164 WERE NOT VISIBLE ON THE ELECTRON DENSITY MAP. THEIR POSITIONS ARE UNCERTAIN
RfactorNum. reflection
obs0.191 9177
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 82 1391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0420.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0180.025
X-RAY DIFFRACTIONp_chiral_restr0.1640.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.2
X-RAY DIFFRACTIONp_multtor_nbd0.1440.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1420.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.16
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
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

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