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- PDB-6eia: PepTSt in complex with HEPES (100 mM) -

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Basic information

Entry
Database: PDB / ID: 6eia
TitlePepTSt in complex with HEPES (100 mM)
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / Alpha helical membrane protein / MFS superfamily / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartinez Molledo, M. / Quistgaard, E.M. / Loew, C.
CitationJournal: Structure / Year: 2018
Title: Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter.
Authors: Martinez Molledo, M. / Quistgaard, E.M. / Flayhan, A. / Pieprzyk, J. / Low, C.
History
DepositionSep 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Jan 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: Di-or tripeptide:H+ symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,35926
Polymers53,6481
Non-polymers6,71125
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-14 kcal/mol
Surface area22260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.490, 110.030, 110.560
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 , 1 types, 1 molecules A

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


Mass: 53648.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8

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Non-polymers , 6 types, 147 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C18H34O4
#6: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 292.15 K / Method: lipidic cubic phase
Details: 0.1 M HEPES pH 7.0, 0.23M ammonium phosphate monobasic, 19% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→49.25 Å / Num. all: 556226 / Num. obs: 42456 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 41.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0651 / Net I/σ(I): 23.25
Reflection shellResolution: 2→2.072 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 2.33 / Num. unique all: 55100 / Num. unique obs: 4167 / CC1/2: 0.766 / % possible all: 99.52

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2D

4d2d


Resolution: 2→49.25 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.2004 2123 5 %
Rwork0.1808 --
obs0.1818 42449 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 459 122 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034146
X-RAY DIFFRACTIONf_angle_d0.7795534
X-RAY DIFFRACTIONf_dihedral_angle_d18.7171521
X-RAY DIFFRACTIONf_chiral_restr0.027605
X-RAY DIFFRACTIONf_plane_restr0.004646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04660.30321390.27122646X-RAY DIFFRACTION99
2.0466-2.09780.23611400.22722664X-RAY DIFFRACTION100
2.0978-2.15450.22211400.20262657X-RAY DIFFRACTION100
2.1545-2.21790.23221400.18742654X-RAY DIFFRACTION100
2.2179-2.28950.21391390.18462653X-RAY DIFFRACTION100
2.2895-2.37130.23141410.18322666X-RAY DIFFRACTION100
2.3713-2.46630.20131400.1752669X-RAY DIFFRACTION100
2.4663-2.57850.19161410.17012670X-RAY DIFFRACTION100
2.5785-2.71450.18451410.16782675X-RAY DIFFRACTION100
2.7145-2.88450.21611420.17632698X-RAY DIFFRACTION100
2.8845-3.10720.24531410.18592695X-RAY DIFFRACTION100
3.1072-3.41980.21411430.18552710X-RAY DIFFRACTION100
3.4198-3.91450.17981420.17242689X-RAY DIFFRACTION100
3.9145-4.93110.18321440.17572749X-RAY DIFFRACTION100
4.9311-49.2690.1891500.18092831X-RAY DIFFRACTION100
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)
10.81590.04970.94091.17130.56170.611-0.0540.031-0.0909-0.14580.12410.0127-0.0322-0.06530.06840.2918-0.01070.01360.29890.01540.2986-34.9232-15.9881-6.0081
22.20770.0710.44480.7086-0.721.8591-0.01280.3721-0.4272-0.11870.1383-0.03810.3495-0.01910.33280.19440.02660.01590.1894-0.07770.1962-17.4213-25.49250.1379
30.72090.265-0.01370.5422-0.2181-0.0285-0.01730.2639-0.1962-0.11840.1546-0.1790.29650.1116-00.45940.0227-0.00890.4233-0.04470.4117-15.4686-28.6382-1.5114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 385 )
3X-RAY DIFFRACTION3chain 'A' and (resid 386 through 478 )

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