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- PDB-6ei3: Crystal structure of auto inhibited POT family peptide transporter -

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Basic information

Entry
Database: PDB / ID: 6ei3
TitleCrystal structure of auto inhibited POT family peptide transporter
ComponentsProton-dependent oligopeptide transporter family proteinProton-dependent oligopeptide transporter
KeywordsMEMBRANE PROTEIN / POT family / Peptide transport / Major Facilitator Superfamily
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / Oligopeptide transporter
Similarity search - Component
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNewstead, S. / Brinth, A. / Vogeley, L. / Caffrey, M.
Funding support United Kingdom, Ireland, United States, 3items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
Science Foundation Ireland12/IA/1255 Ireland
National Institutes of HealthR01GM053148 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Proton movement and coupling in the POT family of peptide transporters.
Authors: Parker, J.L. / Li, C. / Brinth, A. / Wang, Z. / Vogeley, L. / Solcan, N. / Ledderboge-Vucinic, G. / Swanson, J.M.J. / Caffrey, M. / Voth, G.A. / Newstead, S.
History
DepositionSep 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Proton-dependent oligopeptide transporter family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,97618
Polymers56,6301
Non-polymers5,34617
Water5,188288
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 area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.060, 65.230, 70.340
Angle α, β, γ (deg.)90.000, 96.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-891-

HOH

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Components

#1: Protein Proton-dependent oligopeptide transporter family protein / Proton-dependent oligopeptide transporter


Mass: 56630.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: XCCB100_2892 / Plasmid: pWaldo-GFPd / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q8PAS2*PLUS
#2: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C18H34O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 292 K / Method: lipidic cubic phase / pH: 8.5
Details: 100 mM TrisHCl, 120 mM ammonium tartrate, 20 %(v/v) PEG 400, pH 8.5

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 2.1→24.65 Å / Num. obs: 36377 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 36.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.035 / Rrim(I) all: 0.103 / Net I/σ(I): 15.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.154.60.6861230126550.7820.3540.7742.599.9
9.39-24.658.50.03235514160.9990.0120.03451.994.6

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4APS

4aps


Resolution: 2.1→24.65 Å / Cor.coef. Fo:Fc: 0.9515 / Cor.coef. Fo:Fc free: 0.9406 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 1816 4.99 %RANDOM
Rwork0.1792 ---
obs0.1809 36377 99.95 %-
Displacement parametersBiso max: 138.73 Å2 / Biso mean: 45.29 Å2 / Biso min: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.9554 Å20 Å21.2052 Å2
2--3.4976 Å20 Å2
3----0.5422 Å2
Refine analyzeLuzzati coordinate error obs: 0.235 Å
Refinement stepCycle: final / Resolution: 2.1→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 346 288 4620
Biso mean--81.19 55.92 -
Num. residues----511
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1620SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes654HARMONIC5
X-RAY DIFFRACTIONt_it4459HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion536SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5389SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4459HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5971HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion18.04
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2701 155 5.29 %
Rwork0.2101 2774 -
all0.2131 2929 -
obs--99.9 %
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)
11.114-0.0648-0.24841.3674-0.00460.70790.0636-0.1047-0.03560.0232-0.1223-0.1482-0.03560.11540.0587-0.139-0.0169-0.0234-0.03910.0385-0.1238140.124629.7394154.6612
21.5018-0.0007-0.35741.1189-0.02821.29610.00490.00660.05560.02290.0228-0.003-0.0647-0.0171-0.02770.0472-0.0601-0.1414-0.06940.0161-0.0664129.73133.9371154.4479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|16-529}A16 - 529
2X-RAY DIFFRACTION2{ A|601-617 }A601 - 617

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