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

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Basic information

Entry
Database: PDB / ID: 7atx
TitleStructure of P. aeruginosa PBP3 in complex with a benzoxaborole (Compound 4)
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-S1B / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.795 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 1, 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 1.3Nov 13, 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:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,3292
Polymers58,0271
Non-polymers3021
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.916, 83.029, 89.531
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-S1B / 4-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborole-6-carbonyl)-1,3,3-trimethylpiperazin-2-one / 1,3,3-trimethyl-4-[(1-oxidanyl-3H-2,1-benzoxaborol-6-yl)carbonyl]piperazin-2-one / 4-(1-hydroxy-1,3-dihydro-2,1-benzoxaborole-6-carbonyl)-1,3,3-trimethylpiperazin-2-one


Mass: 302.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19BN2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2018 / Details: Mirrors
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.795→60.879 Å / Num. obs: 44743 / % possible obs: 95.5 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Net I/σ(I): 16.4
Reflection shellResolution: 1.796→1.879 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.568 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2238 / CC1/2: 0.457 / Rpim(I) all: 0.605 / % possible all: 52.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSJan 26, 2018data reduction
Aimless0.7.1data scaling
STARANISO1.10.15data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 1.795→60.879 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.224 / SU B: 4.166 / SU ML: 0.123 / Average fsc free: 0.8695 / Average fsc work: 0.8882 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2645 2165 4.839 %
Rwork0.2088 42578 -
all0.211 --
obs-44743 91.884 %
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: 50.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.441 Å20 Å20 Å2
2---0.07 Å2-0 Å2
3----0.372 Å2
Refinement stepCycle: LAST / Resolution: 1.795→60.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 21 150 3961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133911
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173833
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6515317
X-RAY DIFFRACTIONr_angle_other_deg1.2911.5848792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.68120.591203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72915651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2741538
X-RAY DIFFRACTIONr_chiral_restr0.0710.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02906
X-RAY DIFFRACTIONr_nbd_refined0.2040.2764
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23629
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21896
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22059
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2146
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.217
X-RAY DIFFRACTIONr_nbd_other0.1720.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.216
X-RAY DIFFRACTIONr_mcbond_it4.4524.9881994
X-RAY DIFFRACTIONr_mcbond_other4.4514.9881995
X-RAY DIFFRACTIONr_mcangle_it5.9327.4572489
X-RAY DIFFRACTIONr_mcangle_other5.9317.4582490
X-RAY DIFFRACTIONr_scbond_it4.515.6761917
X-RAY DIFFRACTIONr_scbond_other4.5095.6751918
X-RAY DIFFRACTIONr_scangle_it6.9938.2662824
X-RAY DIFFRACTIONr_scangle_other6.9918.2652825
X-RAY DIFFRACTIONr_lrange_it9.28759.1024219
X-RAY DIFFRACTIONr_lrange_other9.2959.0694196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.795-1.8420.402110.3723870.37335300.7150.68411.27480.366
1.842-1.8920.3541300.33825930.33934710.7090.71378.450.34
1.892-1.9470.3611870.31631330.31833690.750.76398.54560.31
1.947-2.0070.3251770.30130820.30232600.8040.82499.96930.284
2.007-2.0720.3051570.25930360.26131930.8610.871000.238
2.072-2.1450.2931540.24429130.24630670.8720.8971000.219
2.145-2.2260.2921430.22728390.2329820.8770.9141000.202
2.226-2.3170.2611520.22326950.22528470.9090.9141000.196
2.317-2.420.3021420.21726160.22127580.8990.921000.193
2.42-2.5380.2671220.20625090.20926310.9180.9321000.188
2.538-2.6750.2741090.2124060.21225160.9130.93299.96030.198
2.675-2.8360.291000.2222760.22323760.9080.9221000.214
2.836-3.0320.286960.21221500.21522460.9090.931000.213
3.032-3.2740.2691210.22319910.22521120.9060.9221000.233
3.274-3.5860.279880.21818550.22119440.9070.92899.94860.237
3.586-4.0070.236730.19216860.19417620.9410.94699.82970.221
4.007-4.6240.227850.17214770.17515620.9440.9591000.214
4.624-5.6540.257520.17812980.18113500.9370.9611000.223
5.654-7.9620.246440.20710160.20910610.9450.95199.90570.27
7.962-60.8790.221220.1946210.1956480.960.95999.22840.291

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