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- PDB-7kgm: C. rodentium YcbB - ertapenem complex -

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Basic information

Entry
Database: PDB / ID: 7kgm
TitleC. rodentium YcbB - ertapenem complex
ComponentsPutative exported protein
KeywordsTRANSFERASE / L / D-transpeptidase / antibiotic
Function / homology
Function and homology information


peptidoglycan biosynthetic process / transferase activity
Similarity search - Function
Scaffold domain / 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 / Putative exported protein
Similarity search - Component
Biological speciesCitrobacter rodentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 17, 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: 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

Downloads & links

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Assembly

Deposited unit
A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8092
Polymers63,3321
Non-polymers4781
Water18010
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)89.997, 117.705, 125.185
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Putative exported protein


Mass: 63331.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter rodentium (strain ICC168) (bacteria)
Strain: ICC168 / Gene: ROD_09941 / Production host: Escherichia coli (E. coli) / References: UniProt: D2TS62
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: C. rodentium YcbB was crystallized at 20C by sitting drop vapour diffusion using 0.2 uL protein solution (8.8 mg/mL purified protein in Buffer A) and 0.1 uL of mother liquor (0.16 M calcium ...Details: C. rodentium YcbB was crystallized at 20C by sitting drop vapour diffusion using 0.2 uL protein solution (8.8 mg/mL purified protein in Buffer A) and 0.1 uL of mother liquor (0.16 M calcium acetate, 0.08 M Sodium Cacodylate pH 6.5, 14% (v/v) PEG 8k, 20% (v/v) glycerol) with the addition of 1mM ertapenem.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→42.876 Å / Num. obs: 20707 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 52.68 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.43 / Net I/σ(I): 3.57
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 1512 / CC1/2: 0.308

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NTW

6ntw


Resolution: 2.6→35.97 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2738 1029 4.97 %
Rwork0.2256 19678 -
obs0.228 20707 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.02 Å2 / Biso mean: 61.6049 Å2 / Biso min: 36.59 Å2
Refinement stepCycle: final / Resolution: 2.6→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 9 10 4033
Biso mean--115.81 55 -
Num. residues----512
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.73710.41191410.3972277099
2.7371-2.90850.46171370.35072767100
2.9085-3.1330.36311700.30982755100
3.133-3.44820.36531340.2492280599
3.4482-3.94690.33541440.21582825100
3.9469-4.97150.20811480.1874282499
4.9715-35.970.20461550.18462932100

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