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- PDB-5ctg: The 3.1 A resolution structure of a eukaryotic SWEET transporter -

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Basic information

Entry
Database: PDB / ID: 5ctg
TitleThe 3.1 A resolution structure of a eukaryotic SWEET transporter
ComponentsBidirectional sugar transporter SWEET2b
KeywordsTRANSPORT PROTEIN / transport / membrane
Function / homology: / SWEET sugar transporter / Sugar efflux transporter for intercellular exchange / sugar transmembrane transporter activity / carbohydrate transport / identical protein binding / plasma membrane / Bidirectional sugar transporter SWEET2b
Function and homology information
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.103 Å
AuthorsTao, Y. / Perry, K. / Feng, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Alfred P. Sloan Foundation United States
CitationJournal: Nature / Year: 2015
Title: Structure of a eukaryotic SWEET transporter in a homotrimeric complex.
Authors: Tao, Y. / Cheung, L.S. / Li, S. / Eom, J.S. / Chen, L.Q. / Xu, Y. / Perry, K. / Frommer, W.B. / Feng, L.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Bidirectional sugar transporter SWEET2b
B: Bidirectional sugar transporter SWEET2b
C: Bidirectional sugar transporter SWEET2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9589
Polymers74,4883
Non-polymers1,4706
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-40 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.830, 142.240, 81.570
Angle α, β, γ (deg.)90.00, 93.36, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTrimer by Crosslinking Studies

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Components

#1: Protein Bidirectional sugar transporter SWEET2b / OsSWEET2b


Mass: 24829.447 Da / Num. of mol.: 3 / Fragment: UNP Residues 1-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: SWEET2B, Os01g0700100, LOC_Os01g50460, OsJ_03146, P0047E11.3, P0454A11.22
Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: Q5N8J1
#2: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 6.5, 30% PEG400, 10mM MnCl2, 5% ethanol
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0717 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0717 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 21149 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.2
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.6 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.103→29.896 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 34.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2913 971 5 %Random selection
Rwork0.2528 ---
obs0.2547 19435 90.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.103→29.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 93 0 5019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095141
X-RAY DIFFRACTIONf_angle_d1.3546976
X-RAY DIFFRACTIONf_dihedral_angle_d181729
X-RAY DIFFRACTIONf_chiral_restr0.06824
X-RAY DIFFRACTIONf_plane_restr0.006840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.103-3.2660.3343850.31191489X-RAY DIFFRACTION51
3.266-3.47030.32751300.29472623X-RAY DIFFRACTION91
3.4703-3.73780.33741560.25722848X-RAY DIFFRACTION99
3.7378-4.11310.30871500.2332872X-RAY DIFFRACTION100
4.1131-4.70630.25721510.20852881X-RAY DIFFRACTION98
4.7063-5.92180.26021420.25112868X-RAY DIFFRACTION99
5.9218-29.89760.29141570.27552883X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -17.1022 Å / Origin y: 2.1215 Å / Origin z: -44.1869 Å
111213212223313233
T1.148 Å20.2189 Å2-0.0615 Å2-2.5479 Å2-0.3311 Å2--0.5447 Å2
L2.2252 °2-0.6495 °2-0.2252 °2-4.2921 °2-1.1835 °2--3.1581 °2
S0.1994 Å °3.4269 Å °-1.0599 Å °-0.9738 Å °-0.8801 Å °-0.4116 Å °0.1748 Å °-0.4863 Å °0.4278 Å °
Refinement TLS groupSelection details: chain 'C'

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