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- PDB-7jwl: Crystal Structure of Pseudomonas aeruginosa Penicillin Binding Pr... -

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Basic information

Entry
Database: PDB / ID: 7jwl
TitleCrystal Structure of Pseudomonas aeruginosa Penicillin Binding Protein 3 (PAE-PBP3) bound to ETX0462
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsANTIBIOTIC / PSEUDOMONAS AERUGINOSA / PBP3 / ETX0462
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
ETX0462 (Bound form) / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMayclin, S.J. / Abendroth, J. / Horanyi, P.S. / Sylvester, M. / Wu, X. / Shapiro, A. / Moussa, S. / Durand-Reville, T.F.
CitationJournal: Nature / Year: 2021
Title: Rational design of a new antibiotic class for drug-resistant infections.
Authors: Durand-Reville, T.F. / Miller, A.A. / O'Donnell, J.P. / Wu, X. / Sylvester, M.A. / Guler, S. / Iyer, R. / Shapiro, A.B. / Carter, N.M. / Velez-Vega, C. / Moussa, S.H. / McLeod, S.M. / Chen, ...Authors: Durand-Reville, T.F. / Miller, A.A. / O'Donnell, J.P. / Wu, X. / Sylvester, M.A. / Guler, S. / Iyer, R. / Shapiro, A.B. / Carter, N.M. / Velez-Vega, C. / Moussa, S.H. / McLeod, S.M. / Chen, A. / Tanudra, A.M. / Zhang, J. / Comita-Prevoir, J. / Romero, J.A. / Huynh, H. / Ferguson, A.D. / Horanyi, P.S. / Mayclin, S.J. / Heine, H.S. / Drusano, G.L. / Cummings, J.E. / Slayden, R.A. / Tommasi, R.A.
History
DepositionAug 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 22, 2021Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 29, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Oct 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5Oct 18, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,7293
Polymers58,3291
Non-polymers4002
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area21690 Å2
Unit cell
Length a, b, c (Å)68.540, 83.950, 90.160
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: 58329.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_ ...Gene: pbpB, ftsI, ftsI_2, ALP65_00912, CAZ10_21230, CGU42_01090, DZ934_06595, DZ962_00565, E4V10_06485, ECC04_026610, ERJ99_003095, FCG96_14995, FLI88_02250, IPC1481_11065, IPC1482_17070, IPC165_24935, IPC170_23205, IPC669_10550, RW109_RW109_05757
Production host: Escherichia coli (E. coli)
References: UniProt: Q51504, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-VMM / ETX0462 (Bound form) / (4R,7S)-7-(N'-hydroxy-N-methylcarbamimidoyl)-1-methyl-4-[(sulfooxy)amino]-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridine-6-carboxylic acid


Mass: 364.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MORPHEUS H12 (293699H12): 12.5% W/V PEG1000, 12.5% W/V PEG3350, 12.5% V/V MPD, 100MM BICINE/TRIZMA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→39.72 Å / Num. obs: 26980 / % possible obs: 99.8 % / Redundancy: 6.098 % / Biso Wilson estimate: 44.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.073 / Χ2: 1.009 / Net I/σ(I): 17.37 / Num. measured all: 164537
Reflection shellResolution: 2.2→39.72 Å / Redundancy: 5.061 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 3.09 / Num. measured obs: 1655 / Num. possible: 357 / Num. unique obs: 327 / CC1/2: 0.999 / Rrim(I) all: 0.03 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829: ???refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wel

4wel


Resolution: 2.2→39.72 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 2063 7.65 %
Rwork0.164 --
obs0.168 26962 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.79 Å2 / Biso mean: 43.87 Å2 / Biso min: 19.83 Å2
Refinement stepCycle: final / Resolution: 2.2→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3724 0 24 206 3954
Biso mean--37.72 46.73 -
Num. residues----500
LS refinement shellResolution: 2.2→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2654 173 -
Rwork0.1975 1566 -
all-1739 -
obs--100 %
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)
1-0.22130.0918-0.2361-0.0476-1.27643.0379-0.020.0275-0.00430.2122-0.2525-0.054-0.32790.15470.220.5981-0.0102-0.05580.3622-0.02380.30798.014830.91235.3207
20.4090.03970.27220.6770.62562.06660.0039-0.0719-0.04680.01680.044-0.00240.09390.0234-0.05160.2252-0.0389-0.00660.25760.0410.26614.772319.7702-8.1726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0
2X-RAY DIFFRACTION2A0

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