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

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Basic information

Entry
Database: PDB / ID: 6ssy
TitleTaurine ABC transporter substrate binding protein TauA from E. coli in complex with 2-Aminoethylphosphonic acid
ComponentsTaurine-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / taurine substrate binding protein / ABC transporter
Function / homology
Function and homology information


cellular response to sulfur starvation / 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-aminoethyl)phosphonic acid / Taurine-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsBeis, K. / Qu, F.
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 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)66,16220
Polymers64,0212
Non-polymers2,14118
Water7,170398
1
A: Taurine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7357
Polymers32,0101
Non-polymers7256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Taurine-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,42713
Polymers32,0101
Non-polymers1,41712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.100, 71.640, 164.550
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: Met in position 1 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-P7I / (2-aminoethyl)phosphonic acid


Mass: 125.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8NO3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane, 20% (w/v) PEG 3350 + 10 mM 2-AEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.62→65.68 Å / Num. obs: 68655 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9
Reflection shellResolution: 1.62→1.65 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 3375 / CC1/2: 0.6

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Processing

Software
NameClassification
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6STL

6stl


Resolution: 1.62→65.68 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.203 --
Rwork0.168 --
obs-68574 99.68 %
Refinement stepCycle: LAST / Resolution: 1.62→65.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 0 50 398 4962

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