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- PDB-7onx: Crystal structure of PBP3 from P. aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7onx
TitleCrystal structure of PBP3 from P. aeruginosa
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsMEMBRANE PROTEIN / PBP3 / peptidoglycan synthesis
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 / 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
Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 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

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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)58,1066
Polymers57,6161
Non-polymers4915
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint4 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.569, 82.205, 91.398
Angle α, β, γ (deg.)90.000, 116.256, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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.: 1
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) (bacteria)
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) (bacteria)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8 mg/ml PBP3, 0.1 M sodium sulfate, 24% (w/v) Polyvinylpyrrolidone

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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: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.16→44.4 Å / Num. obs: 26404 / % possible obs: 91.4 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rrim(I) all: 0.111 / Net I/σ(I): 7.9
Reflection shellResolution: 2.16→2.34 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1320 / CC1/2: 0.471 / Rrim(I) all: 1.015 / % possible all: 57.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC2

3oc2


Resolution: 2.16→44.4 Å / SU ML: 0.2498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2152 1293 4.9 %
Rwork0.1817 25105 -
obs0.1834 26398 66.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.43 Å2
Refinement stepCycle: LAST / Resolution: 2.16→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 32 146 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293713
X-RAY DIFFRACTIONf_angle_d0.57935053
X-RAY DIFFRACTIONf_chiral_restr0.0429568
X-RAY DIFFRACTIONf_plane_restr0.005670
X-RAY DIFFRACTIONf_dihedral_angle_d11.78721357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.240.4183120.3126230X-RAY DIFFRACTION5.58
2.24-2.350.2803580.27331077X-RAY DIFFRACTION25.93
2.35-2.470.3556790.27551706X-RAY DIFFRACTION40.57
2.47-2.620.3091170.26062343X-RAY DIFFRACTION56.47
2.62-2.830.26411710.2323136X-RAY DIFFRACTION74.97
2.83-3.110.23522070.22513997X-RAY DIFFRACTION95.87
3.11-3.560.22312430.19434164X-RAY DIFFRACTION99.59
3.56-4.480.20271960.15174187X-RAY DIFFRACTION99.37
4.48-44.40.1772100.15414265X-RAY DIFFRACTION99.25
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)
1-0.9655166165831.71589737764-2.17667355819-1.67037717593-1.628630353212.605850853740.206383587398-0.1084290065040.06383557369880.178214487738-0.127512241287-0.0587681608898-0.5383664604340.130665731314-0.2626390675550.925262664340.2016702830290.239921480260.7262155157390.06284054418320.5493970799114.18886827926.8833104247344.405791131
22.21325225048-1.46852479683-0.7472341052773.154801726171.353352860112.23883191653-0.247237081096-0.251015377482-0.3280374137250.4838825336520.1837252194160.4581019191540.3249936825580.08536220136310.04994850783840.255959747392-0.02263560109080.01276676880120.1886064730820.09343067810830.29719516468829.9405400225-5.20925613088.53010954335
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 56:25356 - 2531 - 179
22chain A and resseq 254:561254 - 561180 - 479

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