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- PDB-7onk: Crystal structure of PBP3 from P. aeruginosa in complex with AIC499 -

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Basic information

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


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane => GO:0005886 / proteolysis
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-VL5 / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,84119
Polymers115,2322
Non-polymers2,61017
Water13,511750
1
A: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,18613
Polymers57,6161
Non-polymers1,57012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6556
Polymers57,6161
Non-polymers1,0395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.039, 91.139, 148.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 57615.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (unknown)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (unknown)
References: UniProt: G3XD46, 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.: 2 / Source method: obtained synthetically / Formula: C25H34N8O10S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.48 Å3/Da / Density % sol: 50.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 14 mg/ml PBP3, 20% (v/v) Jeffamine M-2070, 20% (v/v) DMSO, 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: 1.73→46.92 Å / Num. obs: 85337 / % possible obs: 95.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rrim(I) all: 0.094 / Net I/σ(I): 10.9
Reflection shellResolution: 1.731→1.901 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4267 / CC1/2: 0.624 / Rrim(I) all: 0.925 / % possible all: 64.8

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC2
Resolution: 1.73→46.92 Å / SU ML: 0.1605 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2572
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2152 4258 4.99 %
Rwork0.1734 81073 -
obs0.1755 85331 74.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.35 Å2
Refinement stepCycle: LAST / Resolution: 1.73→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7586 0 170 750 8506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00688234
X-RAY DIFFRACTIONf_angle_d1.037511227
X-RAY DIFFRACTIONf_chiral_restr0.05441249
X-RAY DIFFRACTIONf_plane_restr0.00751476
X-RAY DIFFRACTIONf_dihedral_angle_d12.65763094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.615320.337215X-RAY DIFFRACTION0.47
1.75-1.770.383750.3857127X-RAY DIFFRACTION3.53
1.77-1.790.121140.3182287X-RAY DIFFRACTION7.72
1.79-1.820.3563170.3213424X-RAY DIFFRACTION11.69
1.82-1.840.2581290.2792601X-RAY DIFFRACTION16.68
1.84-1.860.3449450.2712834X-RAY DIFFRACTION23.33
1.86-1.890.3106640.25841248X-RAY DIFFRACTION34.69
1.89-1.920.3214830.24981765X-RAY DIFFRACTION48.85
1.92-1.950.29081210.2342278X-RAY DIFFRACTION63.38
1.95-1.980.26871360.2132656X-RAY DIFFRACTION72.75
1.98-2.020.25321370.20622788X-RAY DIFFRACTION77.69
2.02-2.050.23511600.20142976X-RAY DIFFRACTION82.96
2.05-2.090.21031710.19343193X-RAY DIFFRACTION87.74
2.09-2.130.24441990.19693361X-RAY DIFFRACTION93.29
2.13-2.180.23992020.19113479X-RAY DIFFRACTION96.29
2.18-2.230.22021810.19033571X-RAY DIFFRACTION99.31
2.23-2.290.21471990.18283619X-RAY DIFFRACTION100
2.29-2.350.22142040.18923607X-RAY DIFFRACTION100
2.35-2.420.23372020.183610X-RAY DIFFRACTION100
2.42-2.50.23041830.17443650X-RAY DIFFRACTION100
2.5-2.590.22141690.17433651X-RAY DIFFRACTION100
2.59-2.690.21811570.17243687X-RAY DIFFRACTION99.97
2.69-2.810.251970.17223621X-RAY DIFFRACTION99.95
2.81-2.960.22192130.17913648X-RAY DIFFRACTION100
2.96-3.150.21162050.16933661X-RAY DIFFRACTION100
3.15-3.390.21311900.16093673X-RAY DIFFRACTION99.92
3.39-3.730.18451980.15243666X-RAY DIFFRACTION99.97
3.73-4.270.17982100.13993708X-RAY DIFFRACTION99.92
4.27-5.380.18541720.15223767X-RAY DIFFRACTION99.9
5.38-46.920.22462030.18833902X-RAY DIFFRACTION99.68
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3576866543150.543498662983-0.2467340955820.980781748464-0.1117492002860.175091202954-0.1960491026990.0793910087020.415928158063-0.3806325738590.2740676651440.7144864350930.02420534844590.009643778000620.402375360960.286404500388-0.0259252664676-0.04813005888140.09154509495630.1054075789280.697447081213-33.64891584831.1376079267-10.8290576671
20.10845410817-0.5488039924090.1146657333862.73645812666-0.5702305578030.114852396459-0.0862587382410.1713393419160.647164138235-0.3821548145230.05691018029950.791245777436-0.416371573942-0.368011114071-0.3546686740080.7081256711170.192872370287-0.118105542850.4105850558230.2003259996350.893276811875-44.374613791425.5751576533-18.0188191779
31.42028464724-0.390476769874-0.2666016103990.9523371617820.1895704593920.8147212602510.2654235681510.2115881033340.0977804770315-0.415901336068-0.196876828146-0.00571555794573-0.1230932626190.1321894371440.104407339254-0.130540781344-0.1093049778370.109977956103-0.0393050564540.109607113376-0.0574456122909-20.9420584839-14.7688668314-6.97279642833
41.657314908580.00964867208129-0.3262258512941.62455327120.3675605619811.36946854415-0.100480583121-0.323356720472-0.0177148080050.1574403049190.0776899311914-0.3079828867440.1363655045650.2611066487220.1872011291540.0591424326684-0.02646707997560.005603057469280.103816920251-0.0139360087440.0882440732797-18.490550521-12.03104493594.10435221663
50.1177142611850.3309555458840.1396769184841.27878633643-0.05153919761520.230508054716-0.0730764909512-0.0590076870979-0.2950028294420.2068308143730.119332281702-0.9143708296510.3203073507510.200041171076-0.4732722292950.3593916143120.0848792823676-0.0460760962370.155295994407-0.03658699793370.485670867456-15.7790636179-27.347511342530.6155334259
60.9820726395210.00703955976908-0.09062372914682.29967003790.3533945160941.015851233270.01573670093110.1977566182190.109993786647-0.254520712357-0.0616339789478-0.0599907780341-0.155925138048-0.190606562129-0.02349507768610.1417038728980.0309353214783-0.03024216115730.18873521565-0.0113825059280.0617180600982-31.852937992916.916558298726.8198406785
70.9067414395910.0788550551324-0.245350484331.12063026399-0.3857662467220.1930146081370.01587118542320.1138925938680.0110141547973-0.1129997835730.02900223423860.214131755110.0832857661343-0.2903221765172.37137365220.1262977408310.017329353027-0.1455393067250.210976311183-0.151123434446-0.102063174836-38.512817821412.181140919833.5272607056
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 48 through 176 )AA48 - 1761 - 129
22chain 'A' and (resid 177 through 211 )AA177 - 211130 - 164
33chain 'A' and (resid 212 through 489 )AA212 - 489165 - 442
44chain 'A' and (resid 490 through 567 )AA490 - 567443 - 512
55chain 'B' and (resid 52 through 224 )BC52 - 2241 - 173
66chain 'B' and (resid 225 through 481 )BC225 - 481174 - 430
77chain 'B' and (resid 482 through 563 )BC482 - 563431 - 505

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