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- PDB-7onw: Crystal structure of PBP3 from E. coli in complex with AIC499 -

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Basic information

Entry
Database: PDB / ID: 7onw
TitleCrystal structure of PBP3 from E. coli in complex with AIC499
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsPROTEIN BINDING / monobactam / PBP3 / peptidoglycan synthesis / drug complex
Function / homology
Function and homology information


divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization ...divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / 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
PHOSPHATE ION / Chem-VL5 / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsFreischem, S. / Grimm, I. / Weiergraeber, O.H.
CitationJournal: Biomolecules / Year: 2021
Title: Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria.
Authors: Freischem, S. / Grimm, I. / Lopez-Perez, A. / Willbold, D. / Klenke, B. / Vuong, C. / Dingley, A.J. / Weiergraber, O.H.
History
DepositionMay 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,2006
Polymers61,1031
Non-polymers1,0975
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-27 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.904, 106.904, 285.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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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: 61102.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ftsI, pbpB, b0084, JW0082 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AD68, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-VL5 / (2S)-2-[(Z)-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2S)-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxy-3-[4-[N-[(3R)-piperidin-3-yl]carbamimidoyl]phenoxy]propanoic acid / AIC499 (bound)


Mass: 670.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H34N8O10S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mg/ml PBP3, 3% dextran sulfate (M-5000), 0.1 M sodium cacodylate, 5% PEG 8000, 30% (v/v) MPD. 0.5 mM AIC499

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.7→48.64 Å / Num. obs: 14000 / % possible obs: 92.2 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rrim(I) all: 0.101 / Net I/σ(I): 15.4
Reflection shellResolution: 2.704→3.034 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 700 / CC1/2: 0.793 / Rrim(I) all: 1.211 / % possible all: 76.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJP

4bjp


Resolution: 2.7→48.64 Å / SU ML: 0.3103 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 762 5.45 %
Rwork0.2335 13232 -
obs0.2356 13994 51.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 71 6 3584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023656
X-RAY DIFFRACTIONf_angle_d0.67174996
X-RAY DIFFRACTIONf_chiral_restr0.0421570
X-RAY DIFFRACTIONf_plane_restr0.0036653
X-RAY DIFFRACTIONf_dihedral_angle_d10.21481291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.3886150.3947325X-RAY DIFFRACTION6.39
2.91-3.210.3021460.3336947X-RAY DIFFRACTION18.53
3.21-3.670.32921010.27021892X-RAY DIFFRACTION36.83
3.67-4.620.25792690.22774610X-RAY DIFFRACTION89
4.62-48.640.26793310.22415458X-RAY DIFFRACTION99.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22079690271.074495230760.1977685874113.275488719450.5145585141421.24793662880.105424548782-0.346326268959-0.5931911239770.556553048048-0.04764291699180.7982493744580.402881151595-0.423791598213-0.05319545085830.4879304989240.003335625512180.08216874431041.591823597830.3247800595091.0375685082320.4510309726-27.4023953541-0.602362681058
20.7498199399170.08827554377410.07203370523030.4300730805040.02856213736350.192243860744-0.1280851622820.1159859055480.0695350555815-0.2075202963570.342003592414-0.0144749187589-0.098962715650.1076250412510.04868768936530.207834396817-0.298563834624-0.06224759648071.476061568020.1803093773460.34338357286132.99873690638.05640584325-23.8005282271
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain A and resseq 62:20062 - 2001 - 139
22chain A and resseq 201:570201 - 570140 - 485

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