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- PDB-1l97: STRUCTURE OF A HINGE-BENDING BACTERIOPHAGE T4 LYSOZYME MUTANT, IL... -

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Basic information

Entry
Database: PDB / ID: 1l97
TitleSTRUCTURE OF A HINGE-BENDING BACTERIOPHAGE T4 LYSOZYME MUTANT, ILE3-> PRO
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDixon, M. / Shewchuk, L. / Matthews, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile3-->Pro.
Authors: Dixon, M.M. / Nicholson, H. / Shewchuk, L. / Baase, W.A. / Matthews, B.W.
#1: Journal: Nature / Year: 1990
Title: A Mutant T4 Lysozyme Displays Five Different Crystal Conformations
Authors: Faber, H.R. / Matthews, B.W.
#2: Journal: Nature / Year: 1988
Title: Hydrophobic Stabilization in T4 Lysozyme Determined Directly by Multiple Substitutions of Ile 3
Authors: Matsumura, M. / Becktel, W.J. / 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
DepositionFeb 11, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET 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 viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T4 LYSOZYME
B: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)37,2932
Polymers37,2932
Non-polymers00
Water3,621201
1
A: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6461
Polymers18,6461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T4 LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6461
Polymers18,6461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.500, 96.600, 39.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE.
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

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Components

#1: Protein T4 LYSOZYME


Mass: 18646.424 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein11
22 Mphosphate11
30.1 M11NaCl
45-10 mMbeta-mercaptoethanol11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.067

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.167 / Highest resolution: 2 Å
Details: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 0 201 2817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.19 / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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