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- PDB-8rtz: The structure of E. coli penicillin binding protein 3 (PBP3) in c... -

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Basic information

Entry
Database: PDB / ID: 8rtz
TitleThe structure of E. coli penicillin binding protein 3 (PBP3) in complex with a bicyclic peptide inhibitor
Components
  • Bicyclic peptide inhibitor
  • Peptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / Inhibitor / Complex / PBP3 (penicillin binding protein 3) / bicyclic peptide / transpeptidase / peptidoglycan
Function / homology
Function and homology information


divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization ...divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to xenobiotic stimulus / cell division / 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-29N / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsNewman, H. / Rowland, C.E. / Dods, R. / Lewis, N. / Stanway, S.J. / Bellini, D. / Beswick, P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Innovate UK971626Q1 United Kingdom
Innovate UK77556 United Kingdom
Innovate UK82975 United Kingdom
CitationJournal: To Be Published
Title: Discovery and chemical optimisation of a Potent, Bi-cyclic (Bicycle) Antimicrobial Inhibitor of Escherichia coli PBP3
Authors: Rowland, C.E. / Newman, H. / Martin, T.T. / Dods, R. / Bournakas, N. / Wagstaff, J.M. / Lewis, N. / Stanway, S.J. / Blamforth, M. / Kessler, C. / van Rietschoten, K. / Bellini, D. / Roper, D. ...Authors: Rowland, C.E. / Newman, H. / Martin, T.T. / Dods, R. / Bournakas, N. / Wagstaff, J.M. / Lewis, N. / Stanway, S.J. / Blamforth, M. / Kessler, C. / van Rietschoten, K. / Bellini, D. / Roper, D.I. / Lloyd, A.J. / Dowson, C.G. / Skynner, M.J. / Beswick, P. / Dawson, M.
History
DepositionJan 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Peptidoglycan D,D-transpeptidase FtsI
A: Bicyclic peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8823
Polymers38,6262
Non-polymers2551
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-10 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.890, 152.181, 43.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11AAA-749-

HOH

21AAA-853-

HOH

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Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Essential cell division protein FtsI / Murein transpeptidase / Penicillin-binding protein 3 / PBP-3 ...Essential cell division protein FtsI / Murein transpeptidase / Penicillin-binding protein 3 / PBP-3 / Peptidoglycan synthase FtsI


Mass: 37129.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsI, pbpB, b0084, JW0082 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AD68, serine-type D-Ala-D-Ala carboxypeptidase
#2: Protein/peptide Bicyclic peptide inhibitor


Mass: 1496.774 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Bicyclic peptide with a scaffold covalently linking three cysteine residues. C-terminus is capped with an amine.
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-29N / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)triprop-2-en-1-one, bound form


Mass: 255.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris pH 9.0 and 20% (w/v) PEG 6K supplemented with an additive, 30% (w/v) dextran sulphate sodium salt, Mr 5K
Temp details: Crystallised on ice

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→45.04 Å / Num. obs: 50525 / % possible obs: 99.6 % / Redundancy: 12.2 % / CC1/2: 1 / Χ2: 1.01 / Net I/av σ(I): 23.8 / Net I/σ(I): 23.8
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 7.1 % / Num. unique obs: 2315 / CC1/2: 0.749 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→45.04 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.015 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2157 2525 4.999 %
Rwork0.1819 47985 -
all0.184 --
obs-50510 99.58 %
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: 24.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å2-0 Å20 Å2
2---1.971 Å2-0 Å2
3----1.069 Å2
Refinement stepCycle: LAST / Resolution: 1.52→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 18 263 2806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132636
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172589
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6513584
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5745949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8155345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31920.403124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14615429
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg17.939153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2851521
X-RAY DIFFRACTIONr_chiral_restr0.090.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
X-RAY DIFFRACTIONr_nbd_refined0.2280.2521
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22444
X-RAY DIFFRACTIONr_nbtor_refined0.170.21292
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2205
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0750.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3480.214
X-RAY DIFFRACTIONr_nbd_other0.2620.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.220
X-RAY DIFFRACTIONr_mcbond_it2.1742.3011353
X-RAY DIFFRACTIONr_mcbond_other2.1692.31352
X-RAY DIFFRACTIONr_mcangle_it3.2413.4391689
X-RAY DIFFRACTIONr_mcangle_other3.2413.441690
X-RAY DIFFRACTIONr_scbond_it2.8482.71283
X-RAY DIFFRACTIONr_scbond_other2.8472.71284
X-RAY DIFFRACTIONr_scangle_it4.3763.9061889
X-RAY DIFFRACTIONr_scangle_other4.3753.9071890
X-RAY DIFFRACTIONr_lrange_it6.37728.8392971
X-RAY DIFFRACTIONr_lrange_other6.37628.8422972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.3331760.3193345X-RAY DIFFRACTION94.5489
1.56-1.6020.2771800.2693416X-RAY DIFFRACTION100
1.602-1.6490.3151760.2663340X-RAY DIFFRACTION100
1.649-1.6990.2571710.2463245X-RAY DIFFRACTION100
1.699-1.7550.2731650.2183137X-RAY DIFFRACTION100
1.755-1.8170.2371610.1983055X-RAY DIFFRACTION99.9689
1.817-1.8850.221540.192932X-RAY DIFFRACTION100
1.885-1.9620.2081490.1842847X-RAY DIFFRACTION100
1.962-2.0490.2331440.1882727X-RAY DIFFRACTION100
2.049-2.1490.2071360.1872594X-RAY DIFFRACTION100
2.149-2.2650.2071310.1742484X-RAY DIFFRACTION100
2.265-2.4030.2181240.1592359X-RAY DIFFRACTION100
2.403-2.5690.2171180.1562243X-RAY DIFFRACTION100
2.569-2.7740.1981080.162045X-RAY DIFFRACTION100
2.774-3.0390.2751010.1721923X-RAY DIFFRACTION100
3.039-3.3970.201920.1761742X-RAY DIFFRACTION100
3.397-3.9210.173810.1651554X-RAY DIFFRACTION100
3.921-4.7990.165710.1481334X-RAY DIFFRACTION99.9289
4.799-6.7760.195540.1731035X-RAY DIFFRACTION100

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