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- PDB-7q0l: Crystal structure of the peptide transporter YePEPT-K314A at 2.93 A -

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Basic information

Entry
Database: PDB / ID: 7q0l
TitleCrystal structure of the peptide transporter YePEPT-K314A at 2.93 A
ComponentsPeptide transporter YePEPT
KeywordsMEMBRANE PROTEIN / MFS / peptide transporter / solute transporter
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / protein transport / plasma membrane
Similarity search - Function
: / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Peptide transporter YePEPT
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. palearctica YE-P4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.71 Å
AuthorsJeckelmann, J.M. / Stauffer, M. / Ilgue, H. / Boggavarapu, R. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_184980 Switzerland
CitationJournal: Commun Chem / Year: 2022
Title: Peptide transporter structure reveals binding and action mechanism of a potent PEPT1 and PEPT2 inhibitor.
Authors: Stauffer, M. / Jeckelmann, J.M. / Ilgu, H. / Ucurum, Z. / Boggavarapu, R. / Fotiadis, D.
History
DepositionOct 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide transporter YePEPT


Theoretical massNumber of molelcules
Total (without water)56,4521
Polymers56,4521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.981, 101.064, 103.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide transporter YePEPT


Mass: 56451.797 Da / Num. of mol.: 1 / Mutation: K314A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica YE-P4 (bacteria)
Gene: YEP4_02370 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R9TD79

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5 / Details: PEG 300, NaOAc, LiH2PO4, Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→46.124 Å / Num. obs: 21272 / % possible obs: 92.8 % / Redundancy: 5.7 % / CC1/2: 1 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.71-2.8425.71.16910650.42175.1
2.842-2.9495.81.56210630.5234171

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.31 Å46.12 Å
Translation5.31 Å46.12 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W6V

4w6v


Resolution: 2.71→28.8138 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.87
RfactorNum. reflection% reflection
Rfree0.2922 1044 4.93 %
Rwork0.2604 --
obs0.262 21193 80.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.16 Å2 / Biso mean: 80.5952 Å2 / Biso min: 28.56 Å2
Refinement stepCycle: final / Resolution: 2.71→28.8138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 0 0 3681
Num. residues----482
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7101-2.85290.4047550.3252109231
2.8529-3.03150.3612980.3234182752
3.0315-3.26520.37541610.3147307687
3.2652-3.59330.34921800.2691345898
3.5933-4.11190.30441900.24913530100
4.1119-5.17570.23271750.2335351797
5.1757-28.81380.28651850.2667364997
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)
12.3144-0.1923-2.19862.10770.46435.2006-0.018-0.263-0.01560.0086-0.08350.0128-0.07040.33070.06870.28440.03910.02810.44480.0380.3082-10.0225-1.084632.6242
22.28420.0198-2.32331.19250.46676.9302-0.1181-0.5148-0.18280.3142-0.0275-0.19850.58561.22150.04330.6790.0569-0.07480.722-0.06890.71372.95923.743736.0958
33.1746-0.7158-2.02326.6079-1.93733.462-0.0274-0.1113-0.05430.3506-0.4294-1.0835-0.33021.1250.52190.5548-0.0995-0.0650.6273-0.0470.624111.5944-21.069126.2151
44.2667-1.47780.06384.0928-0.84771.2395-0.1022-0.0445-0.16460.02470.14610.18550.2408-0.0974-0.07110.5757-0.07790.02170.4453-0.06710.2859-10.6893-23.556829.2219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 202 )A5 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 257 )A203 - 257
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 287 )A258 - 287
4X-RAY DIFFRACTION4chain 'A' and (resid 288 through 503 )A288 - 503

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