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- PDB-5oxo: PepTSt apo structure -

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Basic information

Entry
Database: PDB / ID: 5oxo
TitlePepTSt apo structure
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 / 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 / CITRIC ACID / Di-/tripeptide transporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,62925
Polymers53,6481
Non-polymers6,98124
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: micro scale thermophoresis binding assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.100, 110.300, 110.700
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 BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q5M4H8

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Non-polymers , 6 types, 201 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 15 / 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.: 177 / 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 %
Crystal growTemperature: 292.15 K / Method: lipidic cubic phase / Details: 0.1 M Sodium citrate pH 4.5, 18% PEG 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→49.36 Å / Num. obs: 45647 / % possible obs: 99.63 % / Redundancy: 13.2 % / Biso Wilson estimate: 37.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1223 / Net I/σ(I): 16.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4474 / CC1/2: 0.592 / % possible all: 99.27

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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: 1.95→49.36 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.48
RfactorNum. reflection% reflection
Rfree0.197 2282 5 %
Rwork0.1805 --
obs0.1813 45641 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 477 177 4180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054116
X-RAY DIFFRACTIONf_angle_d0.8775475
X-RAY DIFFRACTIONf_dihedral_angle_d18.1771518
X-RAY DIFFRACTIONf_chiral_restr0.032600
X-RAY DIFFRACTIONf_plane_restr0.004645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99240.32121410.3272668X-RAY DIFFRACTION99
1.9924-2.03880.34991400.29152670X-RAY DIFFRACTION99
2.0388-2.08980.27441420.2512693X-RAY DIFFRACTION99
2.0898-2.14630.23021390.22092645X-RAY DIFFRACTION99
2.1463-2.20940.22921420.18542694X-RAY DIFFRACTION100
2.2094-2.28070.21761410.18512670X-RAY DIFFRACTION99
2.2807-2.36220.18711420.18422699X-RAY DIFFRACTION100
2.3622-2.45680.20911400.18252662X-RAY DIFFRACTION100
2.4568-2.56860.20041430.1692726X-RAY DIFFRACTION100
2.5686-2.7040.17691420.15392695X-RAY DIFFRACTION100
2.704-2.87340.1871420.15972700X-RAY DIFFRACTION100
2.8734-3.09530.19611440.1642728X-RAY DIFFRACTION100
3.0953-3.40670.18461440.17152735X-RAY DIFFRACTION100
3.4067-3.89950.20251440.16832736X-RAY DIFFRACTION100
3.8995-4.91220.17371450.17622766X-RAY DIFFRACTION100
4.9122-49.37910.18761510.18832872X-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)
10.7702-0.01780.82570.88340.42190.6744-0.057-0.0046-0.0736-0.09070.09260.0323-0.0216-0.0738-0.01430.181-0.01460.00560.17780.00840.185-34.8749-16.1711-5.9183
22.32620.37750.64871.5839-0.31231.39260.00820.4934-0.3169-0.25630.1508-0.21950.31550.1879-0.10440.32360.04940.01450.3235-0.05860.2914-16.3577-26.56170.3203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 241 )
2X-RAY DIFFRACTION2chain 'A' and (resid 242 through 478 )

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