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- PDB-4d2c: Structure of a di peptide bound POT family peptide transporter -

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Basic information

Entry
Database: PDB / ID: 4d2c
TitleStructure of a di peptide bound POT family peptide transporter
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / MAJOR FACILITATOR SUPERFAMILY / PROTON OLIGOPEPTIDE TRANSPORTER (POT) FAMILY / PEPTIDE TRANSPORTER / PEPTIDE COMPLEX
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 / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; ...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 / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / 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 / ALANINE / PHENYLALANINE / PHOSPHATE ION / Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsLyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T.A. / Caffrey, M. / Newstead, S.
CitationJournal: Embo Rep. / Year: 2014
Title: Structural Basis for Polyspecificity in the Pot Family of Proton-Coupled Oligopeptide Transporters.
Authors: Lyons, J.A. / Parker, J.L. / Solcan, N. / Brinth, A. / Li, D. / Shah, S.T. / Caffrey, M. / Newstead, S.
History
DepositionMay 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 2.0Feb 21, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_ref / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 2.2Dec 20, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,95710
Polymers53,7211
Non-polymers2,2369
Water68538
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-6 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.060, 110.330, 110.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 53721.125 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 / Plasmid: PWALDO-GFPD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q5M4H8

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Non-polymers , 6 types, 47 molecules

#2: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 57.66 % / Description: NONE
Crystal growMethod: lipidic cubic phase / pH: 7
Details: 16-23 %(V/V) PEG 400, 0.1 M HEPES PH 7.0, 0.15-0.55 M NH4H2PO4 AND 10 MM ALA-PHE. CRYSTALS WERE GROWN BY THE LCP METHOD USING 7.8 MAG AS HOSTING LIPID.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.47→51.03 Å / Num. obs: 22160 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 46.97 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 2.47→2.53 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4APS

4aps


Resolution: 2.47→51.03 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 27.21 / Stereochemistry target values: ML
Details: RESIDUES 1-5, 268-284, 347-351, 407-422, 473-491 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2658 1159 5.2 %
Rwork0.2222 --
obs0.2246 22135 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.375 Å2
Refinement stepCycle: LAST / Resolution: 2.47→51.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 137 38 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033571
X-RAY DIFFRACTIONf_angle_d0.7574833
X-RAY DIFFRACTIONf_dihedral_angle_d15.3131246
X-RAY DIFFRACTIONf_chiral_restr0.052547
X-RAY DIFFRACTIONf_plane_restr0.004575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4702-2.58260.30531490.25292623X-RAY DIFFRACTION99
2.5826-2.71870.29561390.24532634X-RAY DIFFRACTION99
2.7187-2.8890.28851270.23072646X-RAY DIFFRACTION98
2.889-3.11210.29031260.22982623X-RAY DIFFRACTION98
3.1121-3.42520.24881650.22942599X-RAY DIFFRACTION98
3.4252-3.92070.24931410.21282595X-RAY DIFFRACTION96
3.9207-4.9390.23871640.20682616X-RAY DIFFRACTION97
4.939-51.04090.29211480.22482640X-RAY DIFFRACTION94

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