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- PDB-6ghj: PepTSt in complex with tripeptide Phe-Ala-Gln -

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Basic information

Entry
Database: PDB / ID: 6ghj
TitlePepTSt in complex with tripeptide Phe-Ala-Gln
Components
  • Di-or tripeptide:H+ symporter
  • PHE-ALA-GLN
KeywordsMEMBRANE PROTEIN / MFS / POT / peptide transporter
Function / homology
Function and homology information


tripeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide 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 / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / PHOSPHATE ION / Di-/tripeptide transporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsMartinez Molledo, M. / Quistgaard, E.M. / Loew, C.
Funding support2items
OrganizationGrant numberCountry
European Union653706
Swedish Research Council621-2013-5905
CitationJournal: FEBS Lett. / Year: 2018
Title: Tripeptide binding in a proton-dependent oligopeptide transporter.
Authors: Martinez Molledo, M. / Quistgaard, E.M. / Low, C.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Di-or tripeptide:H+ symporter
B: PHE-ALA-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,33322
Polymers53,1472
Non-polymers5,18720
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Differential scanning fluorimetry Microscale thermophoresis Binding studies with PepTSt single mutants
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-29 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.550, 108.220, 111.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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) / Strain (production host): C41 / References: UniProt: Q5M4H8
#2: Protein/peptide PHE-ALA-GLN


Mass: 364.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 7 types, 121 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H34O4
#8: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 292.15 K / Method: lipidic cubic phase
Details: 0.1-0.3 M HEPES buffer pH 7.5, 250 mM ammonium phosphate monobasic (NH4H2PO4), PEG400 (15-25%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9143 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9143 Å / Relative weight: 1
ReflectionResolution: 2.26→48.69 Å / Num. obs: 29604 / % possible obs: 99.73 % / Redundancy: 10.3 % / Biso Wilson estimate: 40.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.44
Reflection shellResolution: 2.26→2.341 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.19 / CC1/2: 0.871 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDS20180126data reduction
XSCALE20180126data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OXO

5oxo


Resolution: 2.26→48.69 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.69
RfactorNum. reflection% reflection
Rfree0.2224 1453 5 %
Rwork0.1905 --
obs0.1921 29043 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 349 101 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073990
X-RAY DIFFRACTIONf_angle_d0.855342
X-RAY DIFFRACTIONf_dihedral_angle_d12.3782263
X-RAY DIFFRACTIONf_chiral_restr0.048592
X-RAY DIFFRACTIONf_plane_restr0.006626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.26-2.34080.23171430.19052708100
2.3408-2.43450.24221430.18872724100
2.4345-2.54530.20181440.1742731100
2.5453-2.67950.20261430.17122727100
2.6795-2.84730.23961450.1747273999
2.8473-3.06710.19881430.1842731100
3.0671-3.37570.25691460.19052776100
3.3757-3.8640.24111460.18692764100
3.864-4.86760.2371470.19052791100
4.86760.19051530.19052899100

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