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- PDB-7kgn: S. Typhi YcbB - ertapenem complex -

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Basic information

Entry
Database: PDB / ID: 7kgn
TitleS. Typhi YcbB - ertapenem complex
ComponentsL,D-transpeptidase
KeywordsTRANSFERASE / L / D-transpeptidase / antibiotic
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / peptidoglycan biosynthetic process / transferase activity
Similarity search - Function
Scaffold domain / PGBD superfamily / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily
Similarity search - Domain/homology
Chem-1RG / L,D-transpeptidase / Putative periplasmic protein
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsCaveney, N.A. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Antimicrob.Agents Chemother. / Year: 2021
Title: Structural and Cellular Insights into the l,d-Transpeptidase YcbB as a Therapeutic Target in Citrobacter rodentium, Salmonella Typhimurium, and Salmonella Typhi Infections.
Authors: Caveney, N.A. / Serapio-Palacios, A. / Woodward, S.E. / Bozorgmehr, T. / Caballero, G. / Vuckovic, M. / Deng, W. / Finlay, B.B. / Strynadka, N.C.J.
History
DepositionOct 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L,D-transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7442
Polymers64,2671
Non-polymers4781
Water00
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)75.309, 75.309, 194.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein L,D-transpeptidase


Mass: 64266.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: ldtD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W3KZB5, UniProt: Q8ZQB5*PLUS
#2: Chemical ChemComp-1RG / (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid / ERTAPENEM, bound form PRE-ISOMERIZED


Mass: 477.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N3O7S / Comment: medication, antibiotic*YM
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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 298.5 K / Method: vapor diffusion, sitting drop
Details: S. Typhi YcbB was crystallized at 20C by sitting drop vapour diffusion using 1 uL protein solution (9 mg/mL purified protein in Buffer A) and 1 uL of mother liquor (0.1 M Tris pH 8.5, 0.18 M ...Details: S. Typhi YcbB was crystallized at 20C by sitting drop vapour diffusion using 1 uL protein solution (9 mg/mL purified protein in Buffer A) and 1 uL of mother liquor (0.1 M Tris pH 8.5, 0.18 M MgCl2, 17% PEG 8k, 2% ethanol) with the addition of 1mM ertapenem (Millipore Sigma).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.965 Å / Num. obs: 7733 / % possible obs: 83.9 % / Redundancy: 7.96 % / Biso Wilson estimate: 56.737 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.315 / Rrim(I) all: 0.337 / Χ2: 1.018 / Net I/σ(I): 2.83 / Num. measured all: 222947 / Scaling rejects: 1040

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NTW

6ntw


Resolution: 3.6→45.965 Å / SU ML: 0.92 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 53.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3587 757 9.79 %
Rwork0.2833 6976 -
obs0.2909 7733 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.35 Å2 / Biso mean: 144.0694 Å2 / Biso min: 87.22 Å2
Refinement stepCycle: final / Resolution: 3.6→45.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3661 0 33 0 3694
Biso mean--159.21 --
Num. residues----462
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.6004-3.87820.64411340.5455133096
3.8782-4.26820.42551460.3406131995
4.2682-4.88530.39481500.2643139899
4.8853-6.15260.37181610.31931419100
6.1526-45.9650.29131660.21561510100

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