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- PDB-5oxl: PepTSt in complex with dipeptide Ala-Leu -

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Basic information

Entry
Database: PDB / ID: 5oxl
TitlePepTSt in complex with dipeptide Ala-Leu
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / Alpha-helical membrane protein / MFS fold / membrane protein / peptide transporter
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 / LEUCINE / PHOSPHATE ION / Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 7, 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 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_ref / struct_ref_seq / struct_site / 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.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_src_gen.gene_src_strain / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Jan 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,91818
Polymers53,6481
Non-polymers4,27017
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: micro scale thermophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-11 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.300, 110.600, 108.500
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


Mass: 53648.074 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) / Variant (production host): C41 / References: UniProt: Q5M4H8

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Non-polymers , 8 types, 49 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 9 / 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.: 1 / Source method: obtained synthetically / Formula: C18H34O4
#7: Chemical ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#8: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 292.15 K / Method: lipidic cubic phase
Details: 0.1 M HEPES pH 7.0, 0.15 M ammonium phosphate monobasic, 18% (v/v) PEG 400, 5 mM Ala-Leu

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.66→46.27 Å / Num. obs: 19071 / % possible obs: 98.2 % / Redundancy: 3 % / Biso Wilson estimate: 49.82 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1076 / Net I/σ(I): 9.58
Reflection shellResolution: 2.66→2.75 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2881 / CC1/2: 0.72 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2B

4d2b


Resolution: 2.66→46.266 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / Phase error: 24.73
RfactorNum. reflection% reflection
Rfree0.2326 878 4.94 %
Rwork0.2237 --
obs-19071 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.66→46.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 277 32 3786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033845
X-RAY DIFFRACTIONf_angle_d0.7555166
X-RAY DIFFRACTIONf_dihedral_angle_d17.7511354
X-RAY DIFFRACTIONf_chiral_restr0.025575
X-RAY DIFFRACTIONf_plane_restr0.004607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.82480.29851400.28282745X-RAY DIFFRACTION97
2.8248-3.04280.30121480.25962810X-RAY DIFFRACTION99
3.0428-3.3490.2411450.24582785X-RAY DIFFRACTION99
3.349-3.83340.23731430.21392778X-RAY DIFFRACTION98
3.8334-4.82880.22741480.20872850X-RAY DIFFRACTION99
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)
10.7135-0.2247-0.69950.91620.14061.114-0.07060.02040.0597-0.05470.07720.03220.02980.06780.00970.311-0.0120.00550.33580.01110.419634.906715.6953-1.1267
21.9190.2783-0.59632.35890.35061.6762-0.13140.126-0.0338-0.28150.05960.04150.0501-0.07320.03140.3205-0.01170.0210.26960.01870.456832.205210.7107-6.6756
31.278-0.3174-0.97070.7264-0.60271.91830.0291-0.0210.3281-0.1929-0.0358-0.0637-0.21750.3171-0.18950.3364-0.00780.06630.34740.00930.447444.252431.4128-13.7672
42.87220.843-1.01942.23090.54531.2324-0.15550.52210.0996-0.28840.11030.1267-0.2051-0.3367-0.02420.40390.0598-0.00630.43510.0030.463117.689123.34191.361
51.078-0.9495-1.51222.88723.85192.320.51380.44450.1653-0.3640.2817-0.52890.2585-0.0373-0.3640.6414-0.02610.00820.43890.06450.532424.493225.1042-7.3864
63.5160.065-1.49783.71020.19644.776-0.05790.43210.5873-0.157-0.44580.3982-0.6748-0.4991-0.21490.5120.09560.10020.3807-0.01230.62512.300931.61687.4959
71.17220.07752.00127.1724-1.22423.68310.1120.49311.21910.33540.27620.3945-1.1753-0.1822-0.32070.56820.0027-0.0790.43420.01370.523923.787417.3155-4.127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 241 )
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 402 )
5X-RAY DIFFRACTION5chain 'A' and (resid 403 through 444 )
6X-RAY DIFFRACTION6chain 'A' and (resid 445 through 471 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 2 )

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