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- PDB-4uvm: In meso crystal structure of the POT family transporter PepTSo -

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Basic information

Entry
Database: PDB / ID: 4uvm
TitleIn meso crystal structure of the POT family transporter PepTSo
ComponentsGLUTATHIONE UPTAKE TRANSPORTER
KeywordsTRANSPORT PROTEIN / MAJOR FACILLITATOR SUPERFAMILY / PROTON OLIGOPEPTIDE TRANSPORTER (POT) FAMILY / PEPTIDE TRANSPORTER
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / membrane / 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 symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / 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 / Glutathione uptake transporter
Similarity search - Component
Biological speciesSHEWANELLA ONEIDENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLyons, J.A. / Solcan, N. / Caffrey, M. / Newstead, S.
CitationJournal: Structure / Year: 2015
Title: Gating Topology of the Proton-Coupled Oligopeptide Symporters.
Authors: Fowler, P.W. / Orwick-Rydmark, M. / Radestock, S. / Solcan, N. / Dijkman, P.M. / Lyons, J.A. / Kwok, J. / Caffrey, M. / Watts, A. / Forrest, L.R. / Newstead, S.
History
DepositionAug 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.3Jan 10, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE UPTAKE TRANSPORTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2576
Polymers57,6851
Non-polymers1,5725
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.830, 86.830, 219.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GLUTATHIONE UPTAKE TRANSPORTER / PEPTIDE TRANSPORTER


Mass: 57684.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHEWANELLA ONEIDENSIS (bacteria) / Strain: MR-1 / Plasmid: PWALDO-GFPE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q8EKT7
#2: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONTAINS A GLY-SER AND AN ADDITIONAL ENLYFQ FROM C- TERMINAL TEV TAG.

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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: 3.74 Å3/Da / Density % sol: 67.1 % / Description: NONE
Crystal growMethod: lipidic cubic phase / pH: 4.5
Details: 20-23 %(V/V) PEG 400, 0.1 M SODIUM ACETATE PH 4.5-4.8, 0.08-0.12 M SODIUM CITRATE. CRYSTALS WERE GROWN BY THE LCP METHOD USING 7.8 MAG AS THE HOSTING LIPID.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013 / Details: MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3→59.13 Å / Num. obs: 17156 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 83.14 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 3→3.08 Å / Redundancy: 5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XUT

2xut


Resolution: 3→59.135 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 29.41 / Stereochemistry target values: ML / Details: RESIDUES 1-7, 513-524 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.258 866 5.1 %
Rwork0.2203 --
obs0.2222 17091 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.35 Å2
Refinement stepCycle: LAST / Resolution: 3→59.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 110 17 4048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034138
X-RAY DIFFRACTIONf_angle_d0.7715591
X-RAY DIFFRACTIONf_dihedral_angle_d14.9451487
X-RAY DIFFRACTIONf_chiral_restr0.026628
X-RAY DIFFRACTIONf_plane_restr0.005686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.1880.37971450.31192667X-RAY DIFFRACTION99
3.188-3.43420.30291380.26982676X-RAY DIFFRACTION98
3.4342-3.77970.26391550.23392651X-RAY DIFFRACTION97
3.7797-4.32650.26881600.20972681X-RAY DIFFRACTION97
4.3265-5.45030.21961380.20332704X-RAY DIFFRACTION96
5.4503-59.14620.24371300.20492846X-RAY DIFFRACTION95

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