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- PDB-1ov5: T4 Lysozyme Cavity Mutant L99a/M102Q Bound With 2-Allylphenol -

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Basic information

Entry
Database: PDB / ID: 1ov5
TitleT4 Lysozyme Cavity Mutant L99a/M102Q Bound With 2-Allylphenol
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-ALLYLPHENOL / BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWei, B.Q. / Baase, W.A. / Weaver, L.H. / Matthews, B.W. / Shoichet, B.K.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Testing a Flexible-receptor Docking Algorithm in a Model Binding Site
Authors: Wei, B.Q. / Weaver, L.H. / Ferrari, A.M. / Matthews, B.W. / Shoichet, B.K.
#1: Journal: 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
DepositionMar 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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)18,9796
Polymers18,6171
Non-polymers3615
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.800, 60.800, 96.900
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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-2LP / 2-ALLYLPHENOL


Mass: 134.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.7 Å3/Da / Density % sol: 54.05 %

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: UCSD MARK II / Detector: AREA DETECTOR / Date: Dec 1, 2002
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→13 Å / Num. obs: 8950 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.26 Å / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1145 / % possible all: 52

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Processing

Software
NameVersionClassification
SanDiego Multiwiredata collection
SanDiego Multiwiredata reduction
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LGU

1lgu


Resolution: 2.1→13 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection% reflection
obs0.184 8906 68 %
Refinement stepCycle: LAST / Resolution: 2.1→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 20 59 1369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.6

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