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- PDB-6fmy: IMISX-EP of S-PepTSt -

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Basic information

Entry
Database: PDB / ID: 6fmy
TitleIMISX-EP of S-PepTSt
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / Serial crystallography / experimental phasing / in meso crystallization / in situ diffraction data collection / membrane protein structure. / MEMBRANE PROTEIN
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / 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 symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / Major facilitator superfamily domain ...: / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / PHOSPHATE ION / Di-/tripeptide transporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsHuang, C.-Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
Funding support Ireland, Switzerland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
European Union701647 Switzerland
CitationJournal: Commun Biol / Year: 2018
Title: In situ serial crystallography for rapid de novo membrane protein structure determination.
Authors: Huang, C.Y. / Olieric, V. / Howe, N. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Vogeley, L. / Basu, S. / Diederichs, K. / Caffrey, M. / Wang, M.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Di-or tripeptide:H+ symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,30719
Polymers52,7821
Non-polymers5,52518
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-2 kcal/mol
Surface area21190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.220, 110.200, 111.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Di-or tripeptide:H+ symporter


Mass: 52782.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria)
Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8
#2: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 22 %(v/v) PEG- 400, 325 mM ammonium dihydrogen phosphate, 100 mM HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 2.0664 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.7→49.29 Å / Num. obs: 33070 / % possible obs: 100 % / Redundancy: 423.6 % / CC1/2: 1 / Rrim(I) all: 0.32 / Net I/σ(I): 40.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 378 % / Mean I/σ(I) obs: 8.8 / Num. unique obs: 2441 / CC1/2: 0.96 / Rrim(I) all: 1.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.29 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2461 1661 5.02 %
Rwork0.2083 --
obs0.2102 33068 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 320 10 3778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033853
X-RAY DIFFRACTIONf_angle_d0.7055166
X-RAY DIFFRACTIONf_dihedral_angle_d13.6432169
X-RAY DIFFRACTIONf_chiral_restr0.04581
X-RAY DIFFRACTIONf_plane_restr0.004612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6999-2.77940.32051520.23272617X-RAY DIFFRACTION100
2.7794-2.86910.32081410.22642603X-RAY DIFFRACTION100
2.8691-2.97160.28811240.23682634X-RAY DIFFRACTION100
2.9716-3.09060.30851320.23452592X-RAY DIFFRACTION100
3.0906-3.23120.22311270.22282655X-RAY DIFFRACTION100
3.2312-3.40150.2921610.21592598X-RAY DIFFRACTION100
3.4015-3.61460.29021210.21012634X-RAY DIFFRACTION100
3.6146-3.89360.2111400.20742597X-RAY DIFFRACTION100
3.8936-4.28520.21741470.18812616X-RAY DIFFRACTION100
4.2852-4.90480.21651290.18622643X-RAY DIFFRACTION100
4.9048-6.17760.25011430.22072615X-RAY DIFFRACTION100
6.1776-49.40320.2141440.19992603X-RAY DIFFRACTION99

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