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- PDB-6gs1: Crystal structure of peptide transporter DtpA-nanobody in MES buffer -

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Basic information

Entry
Database: PDB / ID: 6gs1
TitleCrystal structure of peptide transporter DtpA-nanobody in MES buffer
Components
  • Dipeptide and tripeptide permease A
  • Nanobody 00
KeywordsMEMBRANE PROTEIN / peptide transporter / complex with nanobody / SLC15 family member
Function / homology
Function and homology information


tripeptide transmembrane transport / dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / protein transport / plasma membrane
Similarity search - Function
Amino acid/peptide transporter family, dipeptide and tripeptide permease 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 / Growth Hormone; Chain: A; ...Amino acid/peptide transporter family, dipeptide and tripeptide permease 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 / 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
Dipeptide and tripeptide permease A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsUral-Blimke, Y. / Flayhan, A. / Loew, C. / Quistgaard, E.M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
European UnioniNEXT grant, project no. 653706
Swedish Research Council621-2013-5905 Sweden
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Structure of Prototypic Peptide Transporter DtpA from E. coli in Complex with Valganciclovir Provides Insights into Drug Binding of Human PepT1.
Authors: Ural-Blimke, Y. / Flayhan, A. / Strauss, J. / Rantos, V. / Bartels, K. / Nielsen, R. / Pardon, E. / Steyaert, J. / Kosinski, J. / Quistgaard, E.M. / Low, C.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptide and tripeptide permease A
H: Nanobody 00


Theoretical massNumber of molelcules
Total (without water)69,3702
Polymers69,3702
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-7 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.460, 120.720, 163.330
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 Dipeptide and tripeptide permease A


Mass: 54969.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dtpA, tppB, ydgR, b1634, JW1626 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P77304
#2: Antibody Nanobody 00


Mass: 14400.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: PEG 600, magnesium chloride, MES buffer, pH 6.5

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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: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.29→48.16 Å / Num. obs: 17262 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.2673 / Net I/σ(I): 6.46
Reflection shellResolution: 3.29→3.408 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4q65

4q65


Resolution: 3.29→48.16 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.11
RfactorNum. reflection% reflection
Rfree0.2629 862 5.01 %
Rwork0.2515 --
obs0.2521 17221 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.29→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 0 1 4577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024689
X-RAY DIFFRACTIONf_angle_d0.4476363
X-RAY DIFFRACTIONf_dihedral_angle_d14.542715
X-RAY DIFFRACTIONf_chiral_restr0.037713
X-RAY DIFFRACTIONf_plane_restr0.004792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2899-3.4960.3451400.33492671X-RAY DIFFRACTION99
3.496-3.76580.34571410.29492666X-RAY DIFFRACTION99
3.7658-4.14460.31241410.27182693X-RAY DIFFRACTION100
4.1446-4.74390.2681430.22812701X-RAY DIFFRACTION99
4.7439-5.9750.27311450.23882759X-RAY DIFFRACTION100
5.975-48.54560.18971520.23112869X-RAY DIFFRACTION99

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