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- PDB-7atm: Structure of P. aeruginosa PBP3 in complex with a phenyl boronic ... -

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Basic information

Entry
Database: PDB / ID: 7atm
TitleStructure of P. aeruginosa PBP3 in complex with a phenyl boronic acid (Compound 1)
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
(3-(1H-tetrazol-5-yl)phenyl)boronic acid / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.582 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 29, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _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)58,3874
Polymers58,0271
Non-polymers3603
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint4 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.845, 80.951, 88.800
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 / Fragment: Periplasmic domain
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-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-RY2 / (3-(1H-tetrazol-5-yl)phenyl)boronic acid / [3-(2H-1,2,3,4-tetrazol-5-yl)phenyl]boronic acid / 3-(1H-Tetrazol-5-yl)phenylboronic Acid / 3-(2H-Tetrazol-5-yl)-phenyl-boronic acid / 3-(TETRAZOL-5-YL)PHENYLBORONIC ACID / Boronic acid,B-[3-(2H-tetrazol-5-yl)phenyl]-


Mass: 189.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7BN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.5 Å3/Da / Density % sol: 50.6 %
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: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2018 / Details: Mirrors
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.58→59.824 Å / Num. obs: 53811 / % possible obs: 95.3 % / Redundancy: 8.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.024 / Net I/σ(I): 15.8
Reflection shellResolution: 1.58→1.715 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.413 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2692 / CC1/2: 0.542 / Rpim(I) all: 0.524 / % possible all: 62.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
Aimless0.7.2data scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
STARANISO1.10.15data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R3X

6r3x


Resolution: 1.582→59.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.222 / SU ML: 0.075 / SU R Cruickshank DPI: 0.111 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 2621 4.9 %RANDOM
Rwork0.1907 ---
obs0.1922 53811 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.54 Å2 / Biso mean: 33.059 Å2 / Biso min: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.13 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.582→59.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 22 235 3882
Biso mean--40.59 38.11 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173583
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.6435142
X-RAY DIFFRACTIONr_angle_other_deg1.4011.5738296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9515495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.32121.204191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38915615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.891532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02791
LS refinement shellResolution: 1.582→1.623 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.348 14 -
Rwork0.358 225 -
obs--4.72 %

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