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- PDB-8fss: Complex Structure of YejA-S481A with Microcin C7 -

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Basic information

Entry
Database: PDB / ID: 8fss
TitleComplex Structure of YejA-S481A with Microcin C7
Components
  • Microcin C7
  • YejA
KeywordsPEPTIDE BINDING PROTEIN/ANTIBIOTIC / Trojan Horse / Microcin / peptide transporter / ANTIBIOTIC / PEPTIDE BINDING 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: 2 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 2.0Feb 19, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _audit_author.name / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.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 / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_comp_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.mon_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YejA
B: Microcin C7


Theoretical massNumber of molelcules
Total (without water)69,4982
Polymers69,4982
Non-polymers00
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-7 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.089, 102.834, 144.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1101-

HOH

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Components

#1: Protein YejA


Mass: 68319.945 Da / Num. of mol.: 1 / Mutation: S481A
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 Microcin C7 / MccC7 / Microcin C51 / McC / MccC51 / Microcin C


Mass: 1178.154 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.: 518 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
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: 2→77 Å / Num. obs: 76964 / % possible obs: 99.1 % / Redundancy: 8.4 % / CC1/2: 0.997 / Net I/σ(I): 30.4
Reflection shellResolution: 2.01→2.08 Å / Num. unique obs: 44755 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
autoPROCdata processing
XDSdata scaling
PHASERphasing
REFMAC5.8refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→76.55 Å / Cor.coef. Fo:Fc: 0.941 / Cross valid method: FREE R-VALUE / ESU R: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rwork0.21924 --
obs0.21924 44781 98.84 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.265 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å20 Å2-0 Å2
2---3.06 Å20 Å2
3----2.01 Å2
Refinement stepCycle: 1 / Resolution: 2→76.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4671 0 80 518 5269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0124901
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.6776676
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72521.702282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21115729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9531537
X-RAY DIFFRACTIONr_chiral_restr0.2470.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023805
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.882.6632285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.1933.9732852
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5852.9842615
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.47737.0927706
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.29 3277 -
obs--99.27 %

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