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- PDB-7ato: Structure of P. aeruginosa PBP3 in complex with an aryl boronic a... -

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Basic information

Entry
Database: PDB / ID: 7ato
TitleStructure of P. aeruginosa PBP3 in complex with an aryl boronic acid (Compound 2)
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / D / D-transpeptidase / boron-binding / trivalency
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
(5-methyl-1H-indazol-6-yl)boronic acid / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.587 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
DepositionOct 30, 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 20, 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)58,3734
Polymers58,0271
Non-polymers3463
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint1 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.250, 83.158, 90.115
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 PAO1 (bacteria) / 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-RXW / (5-methyl-1H-indazol-6-yl)boronic acid / 5-Methyl-1H-indazole-6-boronic acid / 5-METHYL-1H-INDAZOL-6-YL-6-BORONIC ACID / Boronic acid, B-(5-methyl-1H-indazol-6-yl)-


Mass: 175.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9BN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 8 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: 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: 1.587→61.113 Å / Num. obs: 53748 / % possible obs: 95.5 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.024 / Net I/σ(I): 15.8
Reflection shellResolution: 1.587→1.706 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.329 / Num. unique obs: 2687 / CC1/2: 0.599 / Rpim(I) all: 0.512 / % possible all: 65.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSJan 26, 2018data reduction
Aimless0.7.1data scaling
STARANISO1.10.15data processing
PHASER2.8.3phasing
PDB_EXTRACTV3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 1.587→61.113 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.153 / SU B: 6.906 / SU ML: 0.098 / Average fsc free: 0.9054 / Average fsc work: 0.9327 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2343 2603 4.843 %
Rwork0.1498 51145 -
all0.154 --
obs-53748 76.782 %
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: 41.788 Å2
Baniso -1Baniso -2Baniso -3
1--2.566 Å2-0 Å20 Å2
2--2.039 Å2-0 Å2
3---0.527 Å2
Refinement stepCycle: LAST / Resolution: 1.587→61.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 21 246 4106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133969
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173884
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.6475388
X-RAY DIFFRACTIONr_angle_other_deg1.3821.588904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.18920.529208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5715660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9711539
X-RAY DIFFRACTIONr_chiral_restr0.0840.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02930
X-RAY DIFFRACTIONr_nbd_refined0.2110.2846
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.23799
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21951
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2187
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0890.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.215
X-RAY DIFFRACTIONr_nbd_other0.2160.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1820.221
X-RAY DIFFRACTIONr_mcbond_it8.0243.9372021
X-RAY DIFFRACTIONr_mcbond_other8.0223.9372022
X-RAY DIFFRACTIONr_mcangle_it9.1355.9142526
X-RAY DIFFRACTIONr_mcangle_other9.1355.9152527
X-RAY DIFFRACTIONr_scbond_it9.5594.6931948
X-RAY DIFFRACTIONr_scbond_other9.5584.6931949
X-RAY DIFFRACTIONr_scangle_it11.5646.7772859
X-RAY DIFFRACTIONr_scangle_other11.5636.7762860
X-RAY DIFFRACTIONr_lrange_it11.58749.2224409
X-RAY DIFFRACTIONr_lrange_other11.57249.1194371
X-RAY DIFFRACTIONr_rigid_bond_restr4.84837853
LS refinement shellResolution: 1.587→1.628 Å
RfactorNum. reflection% reflection
Rfree0.615 16 -
Rwork0.364 281 -
obs--5.8053 %

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