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- PDB-7au9: Structure of P. aeruginosa PBP3 in complex with a benzoxaborole (... -

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Basic information

Entry
Database: PDB / ID: 7au9
TitleStructure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 14)
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 / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / 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
Chem-S1E / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.137 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 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,4763
Polymers58,0271
Non-polymers4492
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.700, 82.724, 88.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-S1E / N,N-dibenzyl-1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborole-6-carboxamide / 1-oxidanyl-N,N-bis(phenylmethyl)-3H-2,1-benzoxaborole-6-carboxamide


Mass: 357.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20BNO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.26 %
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: Jan 26, 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: 2.137→60.446 Å / Num. obs: 21028 / % possible obs: 94.1 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.044 / Net I/σ(I): 12.9
Reflection shellResolution: 2.137→2.341 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.311 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1052 / CC1/2: 0.582 / Rpim(I) all: 0.499 / % possible all: 67.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
Aimless0.7.3data scaling
STARANISO2.2.1data processing
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 2.137→60.446 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.993 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / ESU R: 0.424 / ESU R Free: 0.29
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2743 960 4.565 %
Rwork0.1919 20068 -
all0.196 --
obs-21028 73.499 %
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: 48.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.193 Å20 Å20 Å2
2---0.313 Å2-0 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 2.137→60.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 32 97 3860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173668
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6465219
X-RAY DIFFRACTIONr_angle_other_deg1.2311.5818471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6365487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6520.846201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40415633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7691536
X-RAY DIFFRACTIONr_chiral_restr0.0630.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02820
X-RAY DIFFRACTIONr_nbd_refined0.2190.2814
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23631
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21864
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21939
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2140
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.224
X-RAY DIFFRACTIONr_nbd_other0.2320.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2340.210
X-RAY DIFFRACTIONr_mcbond_it3.9044.9181956
X-RAY DIFFRACTIONr_mcbond_other3.9034.9161953
X-RAY DIFFRACTIONr_mcangle_it5.8527.3562437
X-RAY DIFFRACTIONr_mcangle_other5.8487.362437
X-RAY DIFFRACTIONr_scbond_it4.1795.4951891
X-RAY DIFFRACTIONr_scbond_other4.1785.4941892
X-RAY DIFFRACTIONr_scangle_it6.4688.0382781
X-RAY DIFFRACTIONr_scangle_other6.4678.0382782
X-RAY DIFFRACTIONr_lrange_it9.12558.5914202
X-RAY DIFFRACTIONr_lrange_other9.0658.6014195
LS refinement shellResolution: 2.137→2.193 Å
RfactorNum. reflection% reflection
Rfree0.48 1 -
Rwork0.331 59 -
obs--2.893 %

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