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

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Basic information

Entry
Database: PDB / ID: 7onz
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: 1.86 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)57,8003
Polymers57,6161
Non-polymers1842
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-1 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.492, 37.455, 82.752
Angle α, β, γ (deg.)90.000, 112.573, 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 9 mg/ml PBP3, 0.2 M potassium/sodium tartrate, 20% (w/v) PEG 3350, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.858→40.751 Å / Num. obs: 19031 / % possible obs: 74.8 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rrim(I) all: 0.071 / Net I/σ(I): 12.3
Reflection shellResolution: 1.858→2.091 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 952 / CC1/2: 0.772 / Rrim(I) all: 0.966 / % possible all: 3.6

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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
STARANISOdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC2

3oc2


Resolution: 1.86→40.75 Å / SU ML: 0.2602 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2585 947 4.98 %
Rwork0.2091 18084 -
obs0.2115 19031 51.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.99 Å2
Refinement stepCycle: LAST / Resolution: 1.86→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 12 134 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253751
X-RAY DIFFRACTIONf_angle_d0.60135106
X-RAY DIFFRACTIONf_chiral_restr0.044585
X-RAY DIFFRACTIONf_plane_restr0.0049674
X-RAY DIFFRACTIONf_dihedral_angle_d12.1061356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.960.492360.4011115X-RAY DIFFRACTION2.35
1.96-2.080.3632300.2842675X-RAY DIFFRACTION13.54
2.08-2.240.356870.28961420X-RAY DIFFRACTION29.04
2.24-2.460.29131140.28652062X-RAY DIFFRACTION41.88
2.46-2.820.29031980.26643697X-RAY DIFFRACTION74.25
2.82-3.550.27432400.22334996X-RAY DIFFRACTION99.52
3.55-40.750.22712720.17045119X-RAY DIFFRACTION99.28
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)
11.43470777417-0.9627143863021.37463711070.751733304395-0.8853974465621.32623000571-0.237287200897-0.3460913298960.3704408197620.1806125109360.140796822161-0.1590404089610.00395746032479-0.3654644254970.1471252324410.1803602563520.0201625726404-0.004362872829310.4188313126490.03245397871720.22187742664332.30211443891.8355449036334.1290245131
21.085698304110.1531053559350.1836553801061.35314234232-0.5339905862613.04665174860.132253511504-0.15983358855-0.193545436452-0.136776963111-0.101563268978-0.1459000181850.4075639408090.0501872357124-0.06439754595190.1756434535180.08051795504170.00558984023050.1478380194710.1136584791990.19078799985420.4527976226-0.0591794504512-10.5136083451
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 54:22454 - 2241 - 171
22chain A and resseq 225:560225 - 560172 - 493

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