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- PDB-4tpj: Selectivity mechanism of a bacterial homologue of the human drug ... -

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Basic information

Entry
Database: PDB / ID: 4tpj
TitleSelectivity mechanism of a bacterial homologue of the human drug peptide transporters PepT1 and PepT2
Components
  • ALA-ALA-ALA
  • Proton:oligopeptide symporter POT family
KeywordsMEMBRANE PROTEIN / secondary active transporter / complex
Function / homology
Function and homology information


dipeptide 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 / MFS general substrate transporter like domains / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Proton:oligopeptide symporter POT family
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
Shewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsGuettou, F. / Quistgaard, E. / Raba, M. / Moberg, P. / Low, C. / Nordlund, P.
Funding support Sweden, Singapore, 4items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Swedish Cancer Society Sweden
EDICT Sweden
NRF-CRP Singapore
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2.
Authors: Guettou, F. / Quistgaard, E.M. / Raba, M. / Moberg, P. / Low, C. / Nordlund, P.
History
DepositionJun 7, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Aug 27, 2014Group: Data collection / Other
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 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: Proton:oligopeptide symporter POT family
B: Proton:oligopeptide symporter POT family
C: ALA-ALA-ALA
E: ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5088
Polymers114,9114
Non-polymers1,5974
Water00
1
A: Proton:oligopeptide symporter POT family
E: ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9663
Polymers57,4552
Non-polymers5111
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-2 kcal/mol
Surface area19080 Å2
MethodPISA
2
B: Proton:oligopeptide symporter POT family
C: ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5425
Polymers57,4552
Non-polymers1,0873
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-1 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.990, 107.560, 203.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proton:oligopeptide symporter POT family


Mass: 57224.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1277 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EHE6
#2: Protein/peptide ALA-ALA-ALA


Mass: 231.249 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Production host: Escherichia coli (E. coli)
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M phosphate citrate pH 4.5, 46% PEG300, 0.12M ZnCl2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→47.56 Å / Num. obs: 25529 / % possible obs: 86.9 % / Redundancy: 14.7 % / Net I/σ(I): 22.8
Reflection shellResolution: 3.2→3.28 Å / Mean I/σ(I) obs: 2.42 / Num. measured obs: 8600 / Num. unique all: 587 / CC1/2: 0.739 / % possible all: 27.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEP

4lep


Resolution: 3.201→47.558 Å / SU ML: 0.46 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 35.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2904 1299 5.09 %
Rwork0.2435 --
obs0.2458 25519 86.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.201→47.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6828 0 106 0 6934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117107
X-RAY DIFFRACTIONf_angle_d1.4259682
X-RAY DIFFRACTIONf_dihedral_angle_d15.6212480
X-RAY DIFFRACTIONf_chiral_restr0.0561119
X-RAY DIFFRACTIONf_plane_restr0.0071158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2009-3.32910.4336560.2744102434
3.3291-3.48050.321050.2735189962
3.4805-3.6640.32971430.2506255785
3.664-3.89340.34591680.23383061100
3.8934-4.19390.27431590.23183079100
4.1939-4.61560.25741550.20493084100
4.6156-5.28270.26551640.19973113100
5.2827-6.65280.29151710.29063141100
6.65280.29021780.26683262100
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)
11.5021-0.76021.45646.1096-0.38472.76960.0417-0.40840.16030.6378-0.156-0.06030.0972-0.08560.10770.65-0.09640.21570.597-0.08240.440338.0816-63.7925-23.8176
21.2706-0.25850.31523.73970.07631.25460.1609-0.41520.05010.5767-0.14070.36350.0791-0.4905-0.02530.6287-0.1240.26790.6751-0.02750.535421.7894-16.8619-30.468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B
2X-RAY DIFFRACTION2chain A

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