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- PDB-1li3: T4 lysozyme mutant L99A/M102Q bound by 3-chlorophenol -

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Basic information

Entry
Database: PDB / ID: 1li3
TitleT4 lysozyme mutant L99A/M102Q bound by 3-chlorophenol
ComponentsLysozyme
KeywordsHYDROLASE / Glycosidase / Bacteriolytic enzyme
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
3-CHLOROPHENOL / BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWei, B.Q. / Baase, W.A. / Weaver, L.H. / Matthews, B.W. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: A Model Binding Site for Testing Scoring Functions in Molecular Docking
Authors: Wei, B.Q. / Baase, W.A. / Weaver, L.H. / Matthews, B.W. / Shoichet, B.K.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9736
Polymers18,6171
Non-polymers3565
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.820, 60.820, 97.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lysozyme / / Lysis protein / Muramidase / Endolysin


Mass: 18617.320 Da / Num. of mol.: 1 / Mutation: L99A, M102Q
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-3CH / 3-CHLOROPHENOL / Chlorophenol


Mass: 128.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5ClO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Lipscomb, L.A., (1998) Protein Sci., 7, 765. / PH range low: 7.1 / PH range high: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Msodium phosphate1drop
20.55 M1dropNaCl
30.02 %1dropNaN3
450 mMoxidized beta-mercaptoethanol1reservoir
550 mMreduced beta-mercaptoethanol1reservoir
61.8-2.0 Msodium/potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 1, 2001 / Details: graphite plus pinhole
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→15 Å / Num. all: 16692 / Num. obs: 16692 / % possible obs: 88 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048 / Net I/σ(I): 9.8
Reflection shellResolution: 1.85→1.99 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2824 / % possible all: 79
Reflection
*PLUS
% possible obs: 88 %
Reflection shell
*PLUS
% possible obs: 79 % / Num. unique obs: 2824

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
TNTrefinement
SDMSdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LGU

1lgu


Resolution: 1.85→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: residues ASN163 and LEU164 are missing in the electron density
RfactorNum. reflection% reflection
Rwork0.185 --
all-16692 -
obs-16692 88 %
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 18 61 1369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg2.6
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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