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- PDB-6lep: Crystal structure of thiosulfate transporter YeeE inactive mutant... -

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Basic information

Entry
Database: PDB / ID: 6lep
TitleCrystal structure of thiosulfate transporter YeeE inactive mutant - C91A
ComponentsSulf_transp domain-containing protein
KeywordsTRANSPORT PROTEIN / Transmembrane / Transporter
Function / homologySulphur transport domain / Sulphur 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Yoshikaie, K. / Sugano, Y. / Takeuchi, A. / Uchino, S.
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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulf_transp domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9086
Polymers36,3701
Non-polymers1,5385
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-2 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.910, 94.610, 101.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

21A-811-

HOH

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Components

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


Mass: 36369.656 Da / Num. of mol.: 1 / Mutation: C91A
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-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 48.5 %
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 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→42.878 Å / Num. obs: 10320 / % possible obs: 91.4 % / Redundancy: 29.277 % / Biso Wilson estimate: 47.588 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.358 / Rrim(I) all: 0.363 / Χ2: 1.049 / Net I/σ(I): 10.14 / Num. measured all: 302137 / Scaling rejects: 14
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
2.6-2.7618.7832.5821.4328588181615220.3262.64383.8
2.76-2.9527.7781.6992.5841862169015070.471.72689.2
2.95-3.1832.531.0894.3646778153914380.6481.10593.4
3.18-3.4933.0520.5937.4846141148213960.8820.60194.2
3.49-3.931.3420.36411.0538802131612380.9710.36994.1
3.9-4.530.6250.21518.0833565117710960.9790.21893.1
4.5-5.5232.0760.19518.353037610049470.9830.19794.3
5.52-7.830.6050.15320.99229848007510.9940.15593.9
7.8-42.87830.6850.0835.73130414724250.9990.0890

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: experiment

Resolution: 2.6→42.878 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.2
RfactorNum. reflection% reflection
Rfree0.2863 1015 10.04 %
Rwork0.2351 --
obs0.2403 10106 89.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.48 Å2 / Biso mean: 43.7468 Å2 / Biso min: 19.63 Å2
Refinement stepCycle: final / Resolution: 2.6→42.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 105 22 2523
Biso mean--55.37 43.18 -
Num. residues----318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.7370.38941290.3211112078
2.737-2.90850.3471330.282118484
2.9085-3.1330.3151440.2765130190
3.133-3.44810.25821500.2375133994
3.4481-3.94680.27351510.2261136394
3.9468-4.97130.2821510.2221136394
4.9713-100.26011570.2049142193
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1104-0.05170.25460.0798-0.25980.88430.0717-0.0307-0.05950.0077-0.01970.0083-0.0780.106100.27990.02930.02690.27830.01110.31640.759622.839761.3936
20.57570.2650.41930.5773-0.21260.65180.0450.3372-0.2579-0.183-0.03260.10560.16160.2146-0.00030.30230.01510.02120.3733-0.05460.351236.886320.775748.8579
30.97760.72910.42410.43530.37661.25240.0150.10320.00810.1321-0.0234-0.0504-0.09570.1055-0.00030.17540.0620.04440.150.00690.214645.774730.999657.9994
40.5958-0.10690.50430.1225-0.24170.67280.0170.5956-0.2304-0.13230.09130.1565-0.0409-0.00410.02860.2998-0.04250.07050.325-0.05380.325138.159322.330541.1985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 214 through 328 )A214 - 328
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 58 )A1 - 58
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 162 )A59 - 162
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 213 )A163 - 213

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