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- PDB-8fsr: Complex Structure of YejA with fMccA -

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Basic information

Entry
Database: PDB / ID: 8fsr
TitleComplex Structure of YejA with fMccA
Components
  • Peptide Precursor of Microcin C7
  • YejA
KeywordsTRANSPORT PROTEIN/ANTIBIOTIC / Trojan Horse / Microcin / peptide transporter / ANTIBIOTIC / TRANSPORT PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


microcin transport / oligopeptide transport / ABC-type oligopeptide transporter activity / peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / defense response to bacterium / membrane
Similarity search - Function
Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle
Similarity search - Domain/homology
Uncharacterized protein YejA / Microcin C7
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsNair, S.K. / Dong, S.-H.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131347 United States
National Natural Science Foundation of China (NSFC)21907046 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Trojan horse peptide conjugates remodel the activity spectrum of clinical antibiotics.
Authors: Luo, S. / Li, X.R. / Gong, X.T. / Kulikovsky, A. / Qu, F. / Beis, K. / Severinov, K. / Dubiley, S. / Feng, X. / Dong, S.H. / Nair, S.K.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 19, 2025Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YejA
B: Peptide Precursor of Microcin C7


Theoretical massNumber of molelcules
Total (without water)68,3732
Polymers68,3732
Non-polymers00
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-1 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.523, 103.121, 144.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein YejA


Mass: 67581.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yejA, b2177, JW2165 / Production host: Escherichia coli (E. coli) / References: UniProt: P33913
#2: Protein/peptide Peptide Precursor of Microcin C7 / MccC7 / Microcin C51 / McC / MccC51 / Microcin C


Mass: 791.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q47505
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop
Details: 90 mM BIS-TRIS pH 6.5, 15% (w/v) PEG MME 5000, and 0.5% (w/v) n-dodecyl-beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 62999 / % possible obs: 98.3 % / Redundancy: 12.4 % / CC1/2: 0.999 / Net I/σ(I): 41.4
Reflection shellResolution: 1.78→1.84 Å / Num. unique obs: 62931 / CC1/2: 0.917

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Processing

Software
NameClassification
PDB_EXTRACTdata extraction
autoPROCdata processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→83.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.464 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22535 3187 5 %RANDOM
Rwork0.18207 ---
obs0.18419 60296 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.881 Å2
Baniso -1Baniso -2Baniso -3
1-5.8 Å20 Å2-0 Å2
2---2.91 Å20 Å2
3----2.88 Å2
Refinement stepCycle: 1 / Resolution: 1.78→83.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 0 486 5256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024932
X-RAY DIFFRACTIONr_bond_other_d0.0020.024415
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9526718
X-RAY DIFFRACTIONr_angle_other_deg1.095310235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.685585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12123.522247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52715785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0741537
X-RAY DIFFRACTIONr_chiral_restr0.1150.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215520
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021112
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2592.752313
X-RAY DIFFRACTIONr_mcbond_other2.232.7482312
X-RAY DIFFRACTIONr_mcangle_it3.1384.112892
X-RAY DIFFRACTIONr_mcangle_other3.1414.1132893
X-RAY DIFFRACTIONr_scbond_it3.4863.0952619
X-RAY DIFFRACTIONr_scbond_other3.4863.0952620
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2024.4893822
X-RAY DIFFRACTIONr_long_range_B_refined6.85832.9055883
X-RAY DIFFRACTIONr_long_range_B_other6.73132.3515742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.821 Å
RfactorNum. reflection% reflection
Rfree0.343 236 -
Rwork0.331 4352 -
obs--97.2 %

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