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- PDB-28sw: Structure of ASBT homologue from Leptospira biflexa in inward-fac... -

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Basic information

Entry
Database: PDB / ID: 28sw
TitleStructure of ASBT homologue from Leptospira biflexa in inward-facing form (Crystal Form 2)
ComponentsPutative transporter, sodium/bile acid transporter family protein
KeywordsMEMBRANE PROTEIN / Membrane Transporter SLC10 family Sodium coupled Bile acid transporter
Function / homologyBile acid:sodium symporter/arsenical resistance protein Acr3 / Bile acid:sodium symporter / Sodium Bile acid symporter family / Sodium/solute symporter superfamily / membrane / Putative transporter, sodium/bile acid transporter family protein
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsLi, C. / Cameron, A.D.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M01116X/1 United Kingdom
National Institutes of Health/Office of the DirectorR01GM118772 United States
CitationJournal: To Be Published
Title: Structure and Mechanism of a bacterial homologue of a bile acid transporter
Authors: Li, C. / Grob, A. / Repa, L. / Huxley, O. / Brotherton, D.H. / Becker, P. / Dadzie, R. / Beckstein, O. / Cameron, A.D.
History
DepositionFeb 17, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transporter, sodium/bile acid transporter family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2313
Polymers33,1851
Non-polymers462
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13160 Å2
Unit cell
Length a, b, c (Å)62.468, 67.095, 75.188
Angle α, β, γ (deg.)90.000, 91.037, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein Putative transporter, sodium/bile acid transporter family protein


Mass: 33184.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains 8 residues left before the 3C cleavage site.
Source: (gene. exp.) Leptospira biflexa (bacteria) / Gene: LEPBI_I0103 / Production host: Escherichia coli (E. coli) / References: UniProt: B0SJT7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 0.32M Lithium chloride 0.1M Sodium citrate pH 5.5, 14% w/vPEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.61991 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61991 Å / Relative weight: 1
ReflectionResolution: 2.92→47.62 Å / Num. obs: 6831 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 45.75 Å2 / CC1/2: 0.972 / CC star: 0.993 / Rmerge(I) obs: 0.3478 / Rpim(I) all: 0.1537 / Rrim(I) all: 0.3812 / Net I/σ(I): 3.99
Reflection shellResolution: 2.92→3.22 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1687 / CC1/2: 0.629 / CC star: 0.879 / Rpim(I) all: 0.487 / Rrim(I) all: 1.214

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→47.62 Å / SU ML: 0.3807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.295 329 4.82 %
Rwork0.2401 6490 -
obs0.2426 6819 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.52 Å2
Refinement stepCycle: LAST / Resolution: 2.92→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 2 0 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01222275
X-RAY DIFFRACTIONf_angle_d1.45543090
X-RAY DIFFRACTIONf_chiral_restr0.0844383
X-RAY DIFFRACTIONf_plane_restr0.0142365
X-RAY DIFFRACTIONf_dihedral_angle_d14.0823814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.680.33191620.26343223X-RAY DIFFRACTION99.68
3.68-47.620.27521670.22793267X-RAY DIFFRACTION99.74

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