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- PDB-5d6k: PepT - CIM -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5d6k
TitlePepT - CIM
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / ALPHA-HELICAL / Major Facilitator Superfamily (MFS) Transporters / PepTSt Oligopeptide-proton symporter (POT family)
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
(2R)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate / (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate / PHOSPHATE ION / Di-/tripeptide transporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMa, P. / Caffrey, M.
Funding support Ireland, Belgium, 2items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
Belgian National Funds for Scientific ResearchWELBIO CR-2012S-04 Belgium
CitationJournal: Nat Protoc / Year: 2017
Title: The cubicon method for concentrating membrane proteins in the cubic mesophase.
Authors: Ma, P. / Weichert, D. / Aleksandrov, L.A. / Jensen, T.J. / Riordan, J.R. / Liu, X. / Kobilka, B.K. / Caffrey, M.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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)56,16212
Polymers52,7821
Non-polymers3,38011
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-5 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.690, 110.910, 112.360
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 BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5M4H8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-97M / (2R)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate


Mass: 328.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H36O4
#4: Chemical ChemComp-97N / (2S)-2,3-dihydroxypropyl (9Z)-hexadec-9-enoate


Mass: 328.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H36O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 17-22.5 %(V/V) PEG 400, 0.1 M HEPES PH 7.0 AND 0.15-0.48 M NH4H2PO4. CRYSTALS WERE GROWN BY THE LCP METHOD USING 9.7 MAG AS HOSTING LIPID.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→50.85 Å / Num. obs: 25142 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 1.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
xia20.3.6.3data reduction
xia20.3.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2B

4d2b


Resolution: 2.4→50.845 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1216 4.84 %
Rwork0.2164 --
obs0.2178 25140 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→50.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 235 19 3721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033819
X-RAY DIFFRACTIONf_angle_d0.765142
X-RAY DIFFRACTIONf_dihedral_angle_d15.9441429
X-RAY DIFFRACTIONf_chiral_restr0.025565
X-RAY DIFFRACTIONf_plane_restr0.003613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.49610.3331410.29682615X-RAY DIFFRACTION99
2.4961-2.60970.29981400.27432614X-RAY DIFFRACTION100
2.6097-2.74730.27471140.25622635X-RAY DIFFRACTION100
2.7473-2.91940.28191100.23252656X-RAY DIFFRACTION100
2.9194-3.14480.24931270.22862659X-RAY DIFFRACTION100
3.1448-3.46120.27051400.2212645X-RAY DIFFRACTION100
3.4612-3.96190.21621560.20732644X-RAY DIFFRACTION100
3.9619-4.99090.23041330.19822676X-RAY DIFFRACTION100
4.9909-50.85640.23351550.19752780X-RAY DIFFRACTION100

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