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- PDB-7auh: Structure of P. aeruginosa PBP3 in complex with vaborbactam -

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Basic information

Entry
Database: PDB / ID: 7auh
TitleStructure of P. aeruginosa PBP3 in complex with vaborbactam
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / D / D-transpeptidase / boron-binding
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
Vaborbactam / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.012 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 3, 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)58,4163
Polymers58,0271
Non-polymers3892
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-0 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.175, 83.659, 89.530
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-4D6 / Vaborbactam / {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid / 2-((3R,6S)-2-hydroxy-3-(2-(thiophen-2-yl)acetamido)-1,2-oxaborinan-6-yl)acetic acid / 2-[(3R,6S)-2-hydroxy-3-[(2-thiophen-2-ylacetyl)amino]oxaborinan-6-yl]acetic acid / 1,2-Oxaborinane-6-acetic acid, 2-hydroxy-3-((2-(2-thienyl)acetyl)amino)-, (3R,6S)-


Mass: 297.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16BNO5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.012→61.126 Å / Num. obs: 25128 / % possible obs: 94 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.027 / Net I/σ(I): 15.5
Reflection shellResolution: 2.012→2.215 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.041 / Num. unique obs: 1257 / CC1/2: 0.679 / Rpim(I) all: 0.429 / % possible all: 62.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSNov 11, 2017data reduction
Aimless0.6.2data scaling
STARANISO1.10.2data processing
PDB_EXTRACT3.27data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 2.012→61.126 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.562 / SU ML: 0.198 / Cross valid method: FREE R-VALUE / ESU R: 0.335 / ESU R Free: 0.261
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2809 1161 4.62 %
Rwork0.2077 23967 -
all0.211 --
obs-25128 72.476 %
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: 48.485 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---0.171 Å2-0 Å2
3----0.309 Å2
Refinement stepCycle: LAST / Resolution: 2.012→61.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 26 107 3974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133968
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173878
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.655385
X-RAY DIFFRACTIONr_angle_other_deg1.2471.5788894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6855507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.0120.524210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14715659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0851539
X-RAY DIFFRACTIONr_chiral_restr0.0670.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02933
X-RAY DIFFRACTIONr_nbd_refined0.2170.2867
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23851
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21890
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22082
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.222
X-RAY DIFFRACTIONr_nbd_other0.2050.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.28
X-RAY DIFFRACTIONr_mcbond_it4.4124.8492019
X-RAY DIFFRACTIONr_mcbond_other4.4134.8482018
X-RAY DIFFRACTIONr_mcangle_it6.4187.2492523
X-RAY DIFFRACTIONr_mcangle_other6.4177.252524
X-RAY DIFFRACTIONr_scbond_it4.3755.41949
X-RAY DIFFRACTIONr_scbond_other4.3745.41950
X-RAY DIFFRACTIONr_scangle_it6.6587.9022860
X-RAY DIFFRACTIONr_scangle_other6.6567.9022861
X-RAY DIFFRACTIONr_lrange_it9.19857.6654333
X-RAY DIFFRACTIONr_lrange_other9.19957.674330
LS refinement shellResolution: 2.012→2.064 Å
RfactorNum. reflection% reflection
Rfree0.36 6 -
Rwork0.315 95 -
obs--4.0063 %

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