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- PDB-5jws: T4 Lysozyme L99A with 1-Hydro-2-ethyl-1,2-azaborine Bound -

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Basic information

Entry
Database: PDB / ID: 5jws
TitleT4 Lysozyme L99A with 1-Hydro-2-ethyl-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
2-ethyl-1,2-dihydro-1,2-azaborinine / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 sensu lato (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)18,7644
Polymers18,5861
Non-polymers1783
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-16 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.130, 60.130, 95.610
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-601-

HOH

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Components

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


Mass: 18586.283 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) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-6OQ / 2-ethyl-1,2-dihydro-1,2-azaborinine


Mass: 106.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10BN
#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.: 321 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.2 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: 1.65→31.87 Å / Num. obs: 23693 / % possible obs: 96 % / Redundancy: 8 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 3.3
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.294 / % possible all: 99.9

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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: 3DMV

3dmv


Resolution: 1.65→31.87 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2328 1205 5.09 %
Rwork0.1944 --
obs0.1964 23691 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.9 Å2 / Biso mean: 18.1885 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: final / Resolution: 1.65→31.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 18 321 1619
Biso mean--16.87 31.06 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061446
X-RAY DIFFRACTIONf_angle_d0.8351953
X-RAY DIFFRACTIONf_chiral_restr0.047212
X-RAY DIFFRACTIONf_plane_restr0.005255
X-RAY DIFFRACTIONf_dihedral_angle_d13.007875
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.7160.41321280.324425742702100
1.716-1.79410.33721620.256825262688100
1.7941-1.88870.26461470.225125642711100
1.8887-2.0070.22041340.196225862720100
2.007-2.16190.19241180.164825882706100
2.1619-2.37940.23061370.169325852722100
2.3794-2.72350.22241610.174925962757100
2.7235-3.43070.18751200.17332543266396
3.4307-31.87590.2285980.21241924202269

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