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- PDB-7z6f: Crystal structure of the substrate-binding protein YejA in comple... -

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Basic information

Entry
Database: PDB / ID: 7z6f
TitleCrystal structure of the substrate-binding protein YejA in complex with peptide fragment
Components
  • YejA
  • degradation peptide VAL-LEU-GLY-GLU-PRO-ARG-TYR-ALA-PHE-ASN-PHE-ASN
KeywordsTRANSPORT PROTEIN / ABC importer / peptide transporter / substrate-binding protein
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 / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBeis, K. / Qu, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N020103/1 United Kingdom
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
DepositionMar 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: YejA
A: degradation peptide VAL-LEU-GLY-GLU-PRO-ARG-TYR-ALA-PHE-ASN-PHE-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4518
Polymers69,0232
Non-polymers4286
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-29 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.531, 76.972, 103.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules EA

#1: Protein YejA


Mass: 67595.109 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 degradation peptide VAL-LEU-GLY-GLU-PRO-ARG-TYR-ALA-PHE-ASN-PHE-ASN


Mass: 1427.583 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: degradation peptide during over expression / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 525 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.05 Å3/Da / Density % sol: 40.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.65→62.19 Å / Num. obs: 68508 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.07 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Net I/σ(I): 7.4
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1 / Num. unique obs: 3281 / CC1/2: 0.5 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICQ, 4ONY

5icq

4ony


Resolution: 1.65→62.19 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2325 3399 5.01 %
Rwork0.1894 64425 -
obs0.1915 67824 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.85 Å2
Refinement stepCycle: LAST / Resolution: 1.65→62.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4855 0 26 519 5400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625104
X-RAY DIFFRACTIONf_angle_d0.81536955
X-RAY DIFFRACTIONf_chiral_restr0.0517715
X-RAY DIFFRACTIONf_plane_restr0.0057904
X-RAY DIFFRACTIONf_dihedral_angle_d5.63674176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.3491640.34092485X-RAY DIFFRACTION92.69
1.67-1.70.41581310.33462578X-RAY DIFFRACTION97.17
1.7-1.720.36221380.3172645X-RAY DIFFRACTION97.89
1.72-1.750.3441480.30992612X-RAY DIFFRACTION97.42
1.75-1.780.31911250.2952601X-RAY DIFFRACTION97.43
1.78-1.810.32881450.27222680X-RAY DIFFRACTION98.33
1.81-1.850.29751200.2662646X-RAY DIFFRACTION98.12
1.85-1.890.34651330.24942674X-RAY DIFFRACTION98.18
1.89-1.930.2971440.23272658X-RAY DIFFRACTION98.59
1.93-1.970.2541420.21812647X-RAY DIFFRACTION98.62
1.97-2.020.23461380.21232670X-RAY DIFFRACTION99.22
2.02-2.080.26251400.22684X-RAY DIFFRACTION99.05
2.08-2.140.22171330.18192701X-RAY DIFFRACTION99.47
2.14-2.210.23621580.18342662X-RAY DIFFRACTION99.16
2.21-2.290.24381340.17782696X-RAY DIFFRACTION99.19
2.29-2.380.22311460.17312686X-RAY DIFFRACTION99.37
2.38-2.490.23111450.17462728X-RAY DIFFRACTION99.41
2.49-2.620.22541560.17112688X-RAY DIFFRACTION99.3
2.62-2.780.20881320.16962724X-RAY DIFFRACTION99.58
2.78-30.20691660.1672706X-RAY DIFFRACTION99.55
3-3.30.20371320.15842755X-RAY DIFFRACTION99.72
3.3-3.770.17661280.152784X-RAY DIFFRACTION99.73
3.77-4.760.18161440.13862807X-RAY DIFFRACTION99.46
4.76-61.870.19311570.17462908X-RAY DIFFRACTION99.51
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)
10.569820965037-0.183156275719-0.06562178970540.866752929540.170319609321.34029209420.02595812462280.008566059432780.00379310446667-0.0670586943456-0.00171000844021-0.07426960855210.02593351928710.0876161020957-0.01949367671730.06679935919190.0235116185735-0.004755494398250.07528380224450.0007395030142680.1013392838075.4101021433818.3532920627123.808047481
20.706474169788-0.673669996944-0.03799553599551.08681856837-0.1247946399380.8573873931240.139958665960.1421301024090.129311753768-0.213361927671-0.12410178418-0.128576987792-0.209214251192-0.02812822523750.04131516353480.187097610740.02855841147180.03256260013650.1134410391240.01556466986840.1112353923421.94589940012.58242224914103.488791231
30.955157081786-0.05119782385360.1175184809271.055359156630.5030990326041.53829071968-0.00200203357328-0.0219496283311-0.0316354141971-0.008231085724150.026523027441-0.08537184416680.103002176790.127302635406-0.02058379155560.07698163318410.01754773673010.01426361734160.08579532912450.02431081814130.097477962142824.7429730463-6.99282283939117.975549915
40.390403403166-0.728286586641-0.08436278030182.60665772097-0.7213479521740.6345307425950.1121790965760.0961707982970.0365399174745-0.228687736212-0.01188779747360.0705195247293-0.124493277785-0.139669023644-0.06318991590580.1802377882940.05170770152340.02742770988240.1666177311750.03004846387960.13202729008815.767832279717.77331851103.946707609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 22 through 265 )
2X-RAY DIFFRACTION2chain 'E' and (resid 266 through 351 )
3X-RAY DIFFRACTION3chain 'E' and (resid 352 through 549 )
4X-RAY DIFFRACTION4chain 'E' and (resid 550 through 602 )

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