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- PDB-28sx: Structure of mutated ASBT homologue from Leptospira biflexa in ou... -

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Basic information

Entry
Database: PDB / ID: 28sx
TitleStructure of mutated ASBT homologue from Leptospira biflexa in outward-facing form (no Bile acid)
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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Putative transporter, sodium/bile acid transporter family protein
Function and homology information
Biological speciesLeptospira biflexa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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)34,0525
Polymers33,2931
Non-polymers7594
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13800 Å2
Unit cell
Length a, b, c (Å)81.819, 110.121, 74.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -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: 33292.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.5 / Details: sodium chloride 0.1M Tris 8.5 24% v/v PEG 350 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.61993 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61993 Å / Relative weight: 1
ReflectionResolution: 2.59→33 Å / Num. obs: 10742 / % possible obs: 99.2 % / Redundancy: 8.1 % / Biso Wilson estimate: 36.45 Å2 / CC1/2: 0.99 / CC star: 0.998 / Rmerge(I) obs: 0.2812 / Rpim(I) all: 0.1031 / Rrim(I) all: 0.2999 / Net I/σ(I): 4.91
Reflection shellResolution: 2.59→2.85 Å / Redundancy: 8 % / Rmerge(I) obs: 1.203 / Num. unique obs: 2620 / CC1/2: 0.837 / CC star: 0.955 / Rpim(I) all: 0.4486 / Rrim(I) all: 1.286 / % possible all: 98.26

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→33 Å / SU ML: 0.3799 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.642
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285 539 5.05 %
Rwork0.2528 10138 -
obs0.2544 10677 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.73 Å2
Refinement stepCycle: LAST / Resolution: 2.59→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 30 3 2290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352330
X-RAY DIFFRACTIONf_angle_d0.5213150
X-RAY DIFFRACTIONf_chiral_restr0.0333385
X-RAY DIFFRACTIONf_plane_restr0.0027373
X-RAY DIFFRACTIONf_dihedral_angle_d12.3707851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.850.34261340.3082464X-RAY DIFFRACTION98.26
2.85-3.260.33221330.28282531X-RAY DIFFRACTION99.7
3.26-4.110.27431150.23642540X-RAY DIFFRACTION99.81
4.11-32.840.25751570.23522603X-RAY DIFFRACTION99.03
Refinement TLS params.Method: refined / Origin x: -16.8692128557 Å / Origin y: -25.5992063869 Å / Origin z: 3.5436188249 Å
111213212223313233
T0.729172258071 Å20.0209673901915 Å2-0.00328214062148 Å2-0.262237720777 Å2-0.00139391263914 Å2--0.282809921079 Å2
L1.02640124649 °20.136194274416 °20.453224504414 °2-1.38950146003 °20.145666051292 °2--2.00672029473 °2
S0.160519425159 Å °0.0271421323528 Å °-0.11477100409 Å °0.197328266512 Å °-0.0677702635387 Å °0.0366050293947 Å °0.96829043716 Å °-0.0198403738056 Å °-0.0606044315523 Å °
Refinement TLS groupSelection details: all

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