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- PDB-6leo: Crystal structure of thiosulfate transporter YeeE from Spirochaet... -

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Basic information

Entry
Database: PDB / ID: 6leo
TitleCrystal structure of thiosulfate transporter YeeE from Spirochaeta thermophila
ComponentsSulf_transp domain-containing protein
KeywordsTRANSPORT PROTEIN / Transmembrane / Transporter
Function / homologySulphur transport domain / Sulphur transport / sulfate transport / plasma membrane / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / THIOSULFATE / Thiosulfate transporter TsuA
Function and homology information
Biological speciesSpirochaeta thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.52 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Yoshikaie, K. / Takeuchi, A. / Uchino, S. / Sugano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP19K06526, JP19K22395, JP19H05639 Japan
CitationJournal: Sci Adv / Year: 2020
Title: Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake.
Authors: Tanaka, Y. / Yoshikaie, K. / Takeuchi, A. / Ichikawa, M. / Mori, T. / Uchino, S. / Sugano, Y. / Hakoshima, T. / Takagi, H. / Nonaka, G. / Tsukazaki, T.
History
DepositionNov 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulf_transp domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,72311
Polymers36,4021
Non-polymers3,32110
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-3 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.510, 95.320, 101.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sulf_transp domain-containing protein / YeeE/YedE family protein


Mass: 36401.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaeta thermophila (bacteria) / Gene: Spith_0734 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: G0GAP6
#2: Chemical ChemComp-THJ / THIOSULFATE / Thiosulfate


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: Pentaerythritol-propoxylate, MES, NaCl / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.44 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.44 Å / Relative weight: 1
ReflectionResolution: 2.52→43.134 Å / Num. obs: 12366 / % possible obs: 99.9 % / Redundancy: 87.621 % / Biso Wilson estimate: 45.497 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.631 / Rrim(I) all: 0.635 / Χ2: 1.248 / Net I/σ(I): 14.76 / Num. measured all: 2039899 / Scaling rejects: 528
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.52-2.6785.5626.7521.89317607371337120.3796.792100
2.67-2.8680.7412.9753.19295433366436590.6052.99399.9
2.86-3.0985.5681.6265.4280234327532750.8231.635100
3.09-3.3892.1820.919.46274611297929790.9390.915100
3.38-3.7891.3650.48316.43251619275427540.9860.485100
3.78-4.3690.4960.28726.53218367241324130.9930.289100
4.36-5.3583.5960.23430.26171288204920490.9890.235100
5.35-7.5692.060.18433.81144903157415740.9950.185100
7.56-43.13499.1190.09763.15858378728660.9990.09799.3

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.52→43.134 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2523 1236 10.01 %
Rwork0.2018 --
obs0.2069 12353 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.78 Å2 / Biso mean: 36.597 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 2.52→43.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 230 23 2738
Biso mean--48.3 32.17 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5201-2.6210.32921380.25081234
2.621-2.74030.29051330.22121198
2.7403-2.88470.23371350.20781211
2.8847-3.06540.28391350.21211218
3.0654-3.3020.29351360.19531219
3.302-3.63410.22081370.19291229
3.6341-4.15960.23371370.19481240
4.1596-5.23920.24541390.19561258
5.2392-100.23591460.19721310

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