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- PDB-7kit: Crystal structure of Pseudomonas aeruginosa PBP3 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7kit
TitleCrystal structure of Pseudomonas aeruginosa PBP3 in complex with WCK 4234
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE/Inhibitor/Antibiotic / Inhibitor / cell wall / antibiotic resistance / HYDROLASE / HYDROLASE-Inhibitor-Antibiotic 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 / 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
Chem-C8Y / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.089 Å
Authorsvan den Akker, F.
CitationJournal: Mbio / Year: 2021
Title: Structural Characterization of Diazabicyclooctane beta-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa.
Authors: Rajavel, M. / Kumar, V. / Nguyen, H. / Wyatt, J. / Marshall, S.H. / Papp-Wallace, K.M. / Deshpande, P. / Bhavsar, S. / Yeole, R. / Bhagwat, S. / Patel, M. / Bonomo, R.A. / van den Akker, F.
History
DepositionOct 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1822
Polymers62,9331
Non-polymers2491
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.945, 78.874, 87.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 62933.082 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 (E. coli)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-C8Y / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carbonitrile / open form - WCK 4234


Mass: 249.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.83 Å3/Da / Density % sol: 32.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% polyethylene glycol 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.97928 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.089→29.25 Å / Num. obs: 27862 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.2
Reflection shellResolution: 2.089→2.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.92 / Num. unique obs: 1915 / CC1/2: 0.658 / % possible all: 94.3

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PBQ

3pbq


Resolution: 2.089→29.249 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1450 5.21 %
Rwork0.1951 26362 -
obs0.1975 27812 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.37 Å2 / Biso mean: 37.8607 Å2 / Biso min: 18.18 Å2
Refinement stepCycle: final / Resolution: 2.089→29.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 16 85 3707
Biso mean--39.12 34.28 -
Num. residues----475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0892-2.16390.3391260.2497251196
2.1639-2.25050.2631290.2189263199
2.2505-2.35290.28671510.21492583100
2.3529-2.47690.26031440.21982608100
2.4769-2.6320.2671680.20822587100
2.632-2.8350.28241490.21362629100
2.835-3.120.25441320.20682673100
3.12-3.57080.23731480.19852660100
3.5708-4.49620.22081600.16762672100
4.4962-29.2490.20761430.1808280899

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