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- PDB-7au1: Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (... -

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Basic information

Entry
Database: PDB / ID: 7au1
TitleStructure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 12)
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / D / D-transpeptidase / boron-binding / divalency
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-S08 / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsNewman, H. / Bellini, B. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: J.Med.Chem. / Year: 2021
Title: High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes.
Authors: Newman, H. / Krajnc, A. / Bellini, D. / Eyermann, C.J. / Boyle, G.A. / Paterson, N.G. / McAuley, K.E. / Lesniak, R. / Gangar, M. / von Delft, F. / Brem, J. / Chibale, K. / Schofield, C.J. / Dowson, C.G.
History
DepositionNov 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 22, 2021Group: Data collection / Database references / Non-polymer description
Category: chem_comp / citation ...chem_comp / citation / citation_author / diffrn_source / pdbx_database_proc
Item: _chem_comp.formula / _citation.journal_volume ..._chem_comp.formula / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 2.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,33012
Polymers58,0271
Non-polymers1,30311
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint10 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.038, 81.925, 88.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 58027.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ftsI, pbpB, PA4418 / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase

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Non-polymers , 5 types, 411 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-S08 / 2-(6-(((R)-2-amino-2-oxo-1-phenylethyl)carbamoyl)-1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acetic acid / 2-[(3S)-6-[[(1R)-2-azanyl-2-oxidanylidene-1-phenyl-ethyl]carbamoyl]-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]ethanoic acid


Mass: 368.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17BN2O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% (w/v) polyethylene glycol 3,350, 0.1M Bis-Tris propane pH 6 and 1% (w/v) protamine sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2019 / Details: Mirrors
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.36→60.039 Å / Num. obs: 69775 / % possible obs: 91.7 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Net I/σ(I): 15.1
Reflection shellResolution: 1.36→1.491 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.85 / Num. unique obs: 3488 / Rpim(I) all: 0.381 / Rrim(I) all: 0.935 / % possible all: 62.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 1.36→60.039 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.143 / SU B: 3.811 / SU ML: 0.061 / Average fsc free: 0.9407 / Average fsc work: 0.9566 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2035 3465 4.966 %
Rwork0.1445 66310 -
all0.147 --
obs-69775 65.603 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.581 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å2-0 Å2-0 Å2
2---1.212 Å20 Å2
3---2.933 Å2
Refinement stepCycle: LAST / Resolution: 1.36→60.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 85 400 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134200
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174126
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.6485719
X-RAY DIFFRACTIONr_angle_other_deg1.4621.5839491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.54920.393229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6515706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4041544
X-RAY DIFFRACTIONr_chiral_restr0.0970.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024912
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021000
X-RAY DIFFRACTIONr_nbd_refined0.2190.2813
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23864
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21950
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0660.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.258
X-RAY DIFFRACTIONr_nbd_other0.2880.2168
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1610.22
X-RAY DIFFRACTIONr_mcbond_it3.0931.792071
X-RAY DIFFRACTIONr_mcbond_other3.0941.7882069
X-RAY DIFFRACTIONr_mcangle_it3.6022.6872600
X-RAY DIFFRACTIONr_mcangle_other3.6022.6882601
X-RAY DIFFRACTIONr_scbond_it4.2582.2952129
X-RAY DIFFRACTIONr_scbond_other4.2612.2972130
X-RAY DIFFRACTIONr_scangle_it4.9433.2713092
X-RAY DIFFRACTIONr_scangle_other4.9423.2723093
X-RAY DIFFRACTIONr_lrange_it5.18322.6934639
X-RAY DIFFRACTIONr_lrange_other5.1222.3574565
X-RAY DIFFRACTIONr_rigid_bond_restr10.26738326
LS refinement shellResolution: 1.36→1.395 Å
RfactorNum. reflection% reflection
Rfree0.395 10 -
Rwork0.312 162 -
obs--2.2131 %

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