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- PDB-5jwt: T4 Lysozyme L99A/M102Q with Benzene Bound -

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Basic information

Entry
Database: PDB / ID: 5jwt
TitleT4 Lysozyme L99A/M102Q with Benzene Bound
ComponentsEndolysin
KeywordsHYDROLASE / Phage lysozyme Azaborine
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsLee, H. / Fischer, M. / Shoichet, B.K. / Liu, S.-Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5001989 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics.
Authors: Lee, H. / Fischer, M. / Shoichet, B.K. / Liu, S.Y.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7242
Polymers18,6461
Non-polymers781
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.230, 60.230, 96.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18646.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 2.2 M sodium/potassium phosphate, pH 6.9, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2015
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.41→45.926 Å / Num. obs: 39667 / % possible obs: 99.6 % / Redundancy: 8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 2.9
Reflection shellResolution: 1.41→1.46 Å / Rmerge(I) obs: 0.321 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
d*TREK9.9.9.10Ldata reduction
PHENIXmodel building
PHENIXphasing
d*TREK9.9.9.10Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LGU

1lgu


Resolution: 1.41→45.926 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.58
RfactorNum. reflection% reflection
Rfree0.2429 1997 5.03 %
Rwork0.2201 --
obs0.2213 39665 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.05 Å2 / Biso mean: 18.5688 Å2 / Biso min: 8.69 Å2
Refinement stepCycle: final / Resolution: 1.41→45.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 6 299 1588
Biso mean--13.31 29.15 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051402
X-RAY DIFFRACTIONf_angle_d0.7881891
X-RAY DIFFRACTIONf_chiral_restr0.066205
X-RAY DIFFRACTIONf_plane_restr0.005248
X-RAY DIFFRACTIONf_dihedral_angle_d12.899529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.44520.37641350.33152637X-RAY DIFFRACTION99
1.4452-1.48430.33681330.29432686X-RAY DIFFRACTION100
1.4843-1.5280.36291540.2952634X-RAY DIFFRACTION100
1.528-1.57730.2981390.28622668X-RAY DIFFRACTION100
1.5773-1.63370.29071340.27692707X-RAY DIFFRACTION100
1.6337-1.69910.29051350.26912663X-RAY DIFFRACTION100
1.6991-1.77650.27371520.25482689X-RAY DIFFRACTION100
1.7765-1.87010.32581510.26052664X-RAY DIFFRACTION100
1.8701-1.98730.26791310.23582685X-RAY DIFFRACTION100
1.9873-2.14070.25661410.2152706X-RAY DIFFRACTION100
2.1407-2.35610.22361640.20072682X-RAY DIFFRACTION100
2.3561-2.6970.23111420.21352752X-RAY DIFFRACTION100
2.697-3.39780.21861550.19352739X-RAY DIFFRACTION100
3.3978-45.9260.18441310.1842756X-RAY DIFFRACTION95

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