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- PDB-5oxp: PepTSt in occluded conformation with phosphate ion bound -

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Basic information

Entry
Database: PDB / ID: 5oxp
TitlePepTSt in occluded conformation with phosphate ion bound
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / Alpha-helical membrane protein / membrane protein / MFS fold / 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 / PHOSPHATE ION / Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.372 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 / 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)59,63124
Polymers53,6481
Non-polymers5,98323
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: micro scale thermophoresis binding assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-36 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.600, 110.100, 107.900
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 , 5 types, 60 molecules

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


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: 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
#4: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H34O4
#5: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 292.15 K / Method: lipidic cubic phase
Details: 0.1 M sodium phosphate pH 6.5, 0.25 M ammonium phosphate monobasic, 24% 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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.372→49.04 Å / Num. obs: 24769 / % possible obs: 99.58 % / Redundancy: 6.5 % / Biso Wilson estimate: 58.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09354 / Net I/σ(I): 14.09
Reflection shellResolution: 2.372→2.457 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 2386 / CC1/2: 0.477 / % possible all: 97.27

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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: 2.372→49.037 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.02
RfactorNum. reflection% reflection
Rfree0.2081 1230 4.97 %
Rwork0.1942 --
obs0.1949 24759 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.372→49.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 406 37 4015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094059
X-RAY DIFFRACTIONf_angle_d1.1355419
X-RAY DIFFRACTIONf_dihedral_angle_d17.3981461
X-RAY DIFFRACTIONf_chiral_restr0.041596
X-RAY DIFFRACTIONf_plane_restr0.006636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3723-2.46730.39451350.34612515X-RAY DIFFRACTION98
2.4673-2.57960.30231280.27332614X-RAY DIFFRACTION100
2.5796-2.71550.28221360.22852559X-RAY DIFFRACTION100
2.7155-2.88570.2271410.20912613X-RAY DIFFRACTION100
2.8857-3.10840.28111450.20052585X-RAY DIFFRACTION100
3.1084-3.42120.20921260.18932628X-RAY DIFFRACTION100
3.4212-3.9160.21021420.17142619X-RAY DIFFRACTION100
3.916-4.93310.1721360.17132647X-RAY DIFFRACTION100
4.9331-49.04710.17711410.19622749X-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)
11.53040.2986-1.35572.0438-0.26751.2109-0.16790.1064-0.1368-0.18380.12560.24340.1446-0.03180.04830.4164-0.0021-0.01670.4260.02220.47735.586916.3402-5.1569
25.64740.33480.15632.72160.30714.5366-0.19440.53280.355-0.43720.23870.0669-0.33630.0486-0.02380.46380.02190.06150.382-0.06320.396424.378330.5011-0.0687
34.24690.5287-1.55783.6722-0.64591.7205-0.17770.4894-0.0791-0.63710.09460.14520.0855-0.42950.0170.4441-0.0162-0.01890.4483-0.02920.419414.838220.66750.5461
40.9937-0.89282.42441.7252-4.12619.7610.30890.54020.1247-0.3658-0.01610.4266-0.2987-0.0881-0.40740.78280.2220.00940.69860.04890.63769.434436.8141-7.8484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 241 )
2X-RAY DIFFRACTION2chain 'A' and (resid 242 through 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 449 )
4X-RAY DIFFRACTION4chain 'A' and (resid 450 through 488 )

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