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- PDB-7onn: Crystal structure of PBP3 transpeptidase domain from E. coli in c... -

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Basic information

Entry
Database: PDB / ID: 7onn
TitleCrystal structure of PBP3 transpeptidase domain from E. coli in complex with AIC499
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsPROTEIN BINDING / monobactam / PBP3 / peptidoglycan synthesis / drug complex / transpeptidase domain
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
Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 ...Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-VL5 / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 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 25, 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 1.3Nov 6, 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)45,4614
Polymers43,6971
Non-polymers1,7643
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-7 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.383, 110.383, 142.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-718-

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: 43696.766 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-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mg/ml PBP3, 0.1 M MES, 25% (w/v) PEG 1000, 0.5 mM AIC499

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.92→47.8 Å / Num. obs: 18221 / % possible obs: 95 % / Redundancy: 18.1 % / Biso Wilson estimate: 41.23 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 24.4
Reflection shellResolution: 1.92→2.22 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 911 / CC1/2: 0.783 / Rrim(I) all: 1.602 / % possible all: 74.3

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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: 1.92→47.8 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 935 5.16 %
Rwork0.2233 17193 -
obs0.2256 18128 45.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.23 Å2 / Biso mean: 51.2242 Å2 / Biso min: 25.67 Å2
Refinement stepCycle: final / Resolution: 1.92→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 135 60 3206
Biso mean--61.81 44.92 -
Num. residues----403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-2.020.465340.439595992
2.02-2.140.5122220.3954404628
2.14-2.310.5185340.459766970313
2.31-2.540.3951880.34861617170530
2.54-2.910.35361990.32263221342060
2.91-3.670.30933000.255454165716100
3.67-47.80.21572880.176857356023100
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)
10.05620.1388-0.24782.45780.04621.28590.03280.1018-0.0227-0.36190.13390.4233-0.0949-0.4452-0.16990.4963-0.0941-0.22440.66990.47780.57563.88137.335-19.148
21.1514-0.1464-0.18082.1134-0.77711.6396-0.0789-0.0856-0.1448-0.21490.39230.7630.0378-0.7443-0.35040.5747-0.0546-0.20530.81380.50270.6942-0.45836.895-10.871
30.796-0.48130.57340.9899-0.52260.87130.21590.0711-0.2382-0.23570.09530.21170.343-0.2724-0.19090.5516-0.0399-0.28460.30340.26910.356116.91627.788-13.962
40.8605-0.80920.01481.7327-1.14671.32050.12230.0109-0.2347-0.23290.16920.27940.549-0.1759-0.23260.53330.0263-0.19940.40010.22610.367219.07722.2620.715
53.3415-0.67020.39171.38180.18722.2914-0.1041-0.3609-0.3030.25320.2205-0.35660.81820.297-0.11660.8460.3441-0.12710.740.23570.792238.56716.75215.215
60.3740.08430.23960.6098-0.38030.47360.1095-0.0247-0.2529-0.0483-0.0809-0.18470.26420.25040.02470.58180.286-0.22770.54340.22420.534.6719.5911.132
70.277-0.1667-0.42340.8190.18130.6481-0.0792-0.298-0.22360.30080.2230.13050.3928-0.0991-0.03960.5927-0.0331-0.24490.48090.48120.422918.49722.5438.575
82.9969-0.60081.75910.81420.60512.3568-0.027-0.12520.3981-0.02080.32750.1837-0.1479-0.5302-0.27560.26410.04940.01940.34290.18470.488719.47341.0065.016
91.013-0.0823-0.03021.13680.00121.07750.1633-0.2369-0.1023-0.11960.0488-0.3270.25130.3304-0.20380.25670.1263-0.02320.39260.04470.444637.51231.315-1.303
101.2928-0.14930.15823.8739-0.40321.78120.1229-0.1121-0.314-0.04070.07390.240.5011-0.3137-0.12580.6098-0.0425-0.14140.22630.16790.379524.78820.449-2.724
110.73930.1494-0.4415.4915-0.44081.130.23910.0467-0.0953-0.10610.1651-0.2440.2831-0.0148-0.28430.58870.1022-0.1060.17920.06610.393930.97227.943-11.452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 70:179 )A70 - 179
2X-RAY DIFFRACTION2( CHAIN A AND RESID 180:237 )A180 - 237
3X-RAY DIFFRACTION3( CHAIN A AND RESID 238:288 )A238 - 288
4X-RAY DIFFRACTION4( CHAIN A AND RESID 289:319 )A289 - 319
5X-RAY DIFFRACTION5( CHAIN A AND RESID 320:341 )A320 - 341
6X-RAY DIFFRACTION6( CHAIN A AND RESID 342:382 )A342 - 382
7X-RAY DIFFRACTION7( CHAIN A AND RESID 383:436 )A383 - 436
8X-RAY DIFFRACTION8( CHAIN A AND RESID 437:460 )A437 - 460
9X-RAY DIFFRACTION9( CHAIN A AND RESID 461:491 )A461 - 491
10X-RAY DIFFRACTION10( CHAIN A AND RESID 492:533 )A492 - 533
11X-RAY DIFFRACTION11( CHAIN A AND RESID 534:569 )A534 - 569

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