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- PDB-5jwu: T4 Lysozyme L99A/M102Q with 1,2-Dihydro-1,2-azaborine Bound -

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Basic information

Entry
Database: PDB / ID: 5jwu
TitleT4 Lysozyme L99A/M102Q with 1,2-Dihydro-1,2-azaborine 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
1,2-dihydro-1,2-azaborinine / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 sensu lato (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7964
Polymers18,6461
Non-polymers1503
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-15 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.100, 60.100, 96.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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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 sensu lato (virus)
Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-B20 / 1,2-dihydro-1,2-azaborinine / 1,2-DIHYDRO-1,2-AZABORINE


Mass: 78.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6BN
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 2.1 M sodium/potassium phosphate, pH 7.0, 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: 1.7→45.84 Å / Num. obs: 22416 / % possible obs: 98.1 % / Redundancy: 8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 2.3
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.438 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
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: 1.7→45.84 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.99
RfactorNum. reflection% reflection
Rfree0.2509 1158 5.17 %
Rwork0.2261 --
obs0.2274 22407 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.62 Å2 / Biso mean: 29.85 Å2 / Biso min: 17.95 Å2
Refinement stepCycle: final / Resolution: 1.7→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 8 144 1435
Biso mean--30.17 39.74 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071413
X-RAY DIFFRACTIONf_angle_d1.0021912
X-RAY DIFFRACTIONf_chiral_restr0.039209
X-RAY DIFFRACTIONf_plane_restr0.004251
X-RAY DIFFRACTIONf_dihedral_angle_d12.802540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.77730.34061380.307226752813100
1.7773-1.8710.43261410.331926672808100
1.871-1.98830.38651480.312426612809100
1.9883-2.14180.33681520.281126762828100
2.1418-2.35730.30291550.238526732828100
2.3573-2.69840.24141470.228427022849100
2.6984-3.39950.22771510.20452700285199
3.3995-45.85510.1841260.18732495262186

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