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- PDB-6stl: Taurine ABC transporter substrate binding protein TauA from E. co... -

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Basic information

Entry
Database: PDB / ID: 6stl
TitleTaurine ABC transporter substrate binding protein TauA from E. coli in complex with taurine
ComponentsTaurine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / taurine substrate binding protein / ABC transporter
Function / homology
Function and homology information


cellular response to sulfur starvation / alkanesulfonate transmembrane transport / cellular response to sulfate starvation / taurine transmembrane transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / membrane
Similarity search - Function
Taurine ABC transporter, substrate-binding protein TauA / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Bacterial periplasmic substrate-binding proteins / Solute-binding protein family 3/N-terminal domain of MltF
Similarity search - Domain/homology
IODIDE ION / 2-AMINOETHANESULFONIC ACID / Taurine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsBeis, K. / Qu, F. / Wagner, A. / ElOmari, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N020103/1 United Kingdom
CitationJournal: Biochem.J. / Year: 2019
Title: Desolvation of the substrate-binding protein TauA dictates ligand specificity for the alkanesulfonate ABC importer TauABC.
Authors: Qu, F. / ElOmari, K. / Wagner, A. / De Simone, A. / Beis, K.
History
DepositionSep 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Taurine-binding periplasmic protein
B: Taurine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,04818
Polymers64,0212
Non-polymers2,02716
Water10,881604
1
A: Taurine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,27811
Polymers32,0101
Non-polymers1,26710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Taurine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7707
Polymers32,0101
Non-polymers7606
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.960, 74.092, 164.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Taurine-binding periplasmic protein / Sulfate starvation-induced protein 1 / SSI1


Mass: 32010.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Met22 is from cloning
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tauA, ssiA, yaiR, b0365, JW0357 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47537
#2: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID / Taurine


Mass: 125.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.25 M sodium iodide, 0.1 M Bis-Tris propane, 24% (w/v) PEG 3350 + 10 mM taurine

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9763
SYNCHROTRONDiamond I2322.3751
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELJun 24, 2017
DECTRIS PILATUS 12M2PIXELJun 28, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Silicon crystal
Radiation wavelength
IDWavelength (Å)Relative weight
10.97631
22.37511
Reflection

Entry-ID: 6STL / CC1/2: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.3-67.5313054297.53.20.056111
1.77-65.47452588619.30.12215.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.3-1.330.432.564140.8196.9
1.77-1.810.833.122020.8274

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→43.36 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.183 --
Rwork0.145 --
obs-130403 97.51 %
Refinement stepCycle: LAST / Resolution: 1.3→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 28 606 5148

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