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- PDB-6gz9: Crystal structure of a POT family transporter in complex with pro... -

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Basic information

Entry
Database: PDB / ID: 6gz9
TitleCrystal structure of a POT family transporter in complex with prodrug valacyclovir
ComponentsPeptide ABC transporter permease
KeywordsMEMBRANE PROTEIN / Peptide transporter / prodrug complex
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / membrane => GO:0016020 / 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
Chem-TXC / Peptide ABC transporter permease / Peptide ABC transporter permease
Similarity search - Component
Biological speciesStaphylococcus hominis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMinhas, G.S. / Newstead, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters.
Authors: Minhas, G.S. / Newstead, S.
History
DepositionJul 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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: Peptide ABC transporter permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2752
Polymers53,9511
Non-polymers3241
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.119, 56.576, 99.172
Angle α, β, γ (deg.)90.000, 104.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide ABC transporter permease / POT family peptide transporter / proton coupled peptide transporter


Mass: 53951.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus hominis (bacteria) / Gene: BL313_09825 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: A0A1L8Y4Q3, UniProt: A0A657M1C3*PLUS
#2: Chemical ChemComp-TXC / 2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]ethyl L-valinate / Valacyclovir


Mass: 324.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 26-27% (v/v) PEG 200, 220 mM (NH4)2HPO4, and 110 mM sodium citrate (pH 5.0). Ligand: 40mM valacyclovir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 3.1→58.2 Å / Num. obs: 11917 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 60.92 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.23 / Net I/σ(I): 5.6
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.17 / Num. unique obs: 2145 / CC1/2: 0.547 / Rpim(I) all: 0.94 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
Aimless0.5.27data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EXS

6exs


Resolution: 3.1→58.162 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.76
RfactorNum. reflection% reflection
Rfree0.3055 486 4.13 %
Rwork0.2439 --
obs0.2463 11780 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.79 Å2 / Biso mean: 69.1491 Å2 / Biso min: 33.95 Å2
Refinement stepCycle: final / Resolution: 3.1→58.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 23 6 3796
Biso mean--84.8 55.88 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093884
X-RAY DIFFRACTIONf_angle_d1.1555284
X-RAY DIFFRACTIONf_chiral_restr0.059625
X-RAY DIFFRACTIONf_plane_restr0.007658
X-RAY DIFFRACTIONf_dihedral_angle_d7.3512243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.54860.34581650.285137713936100
3.5486-4.47060.32681730.24523711388499
4.4706-58.1720.26941480.22843812396098

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