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

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Basic information

Entry
Database: PDB / ID: 28sz
TitleStructure of mutated ASBT homologue from Leptospira biflexa in outward-facing form with Deoxycholate
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: 2.52 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)33,7314
Polymers33,2931
Non-polymers4393
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint2 kcal/mol
Surface area12720 Å2
Unit cell
Length a, b, c (Å)55.200, 75.118, 94.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8.5
Details: 0.12M Magnesium formate dihydrate 0.1M Sodium chloride, 0.1M Tris, pH 8.5, 33% v/v PEG 600, supplemented with 1 mM DCA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.61992 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 2.52→58.92 Å / Num. obs: 13781 / % possible obs: 99.23 % / Redundancy: 10.1 % / Biso Wilson estimate: 50.24 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.3455 / Rpim(I) all: 0.1097 / Rrim(I) all: 0.3632 / Net I/σ(I): 3.78
Reflection shellResolution: 2.52→2.72 Å / Redundancy: 9.4 % / Rmerge(I) obs: 2.539 / Num. unique obs: 2641 / CC1/2: 0.606 / CC star: 0.869 / Rpim(I) all: 0.8434 / Rrim(I) all: 2.681 / % possible all: 98.32

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→58.92 Å / SU ML: 0.4124 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2872 667 4.87 %
Rwork0.2746 13027 -
obs0.2753 13694 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.93 Å2
Refinement stepCycle: LAST / Resolution: 2.52→58.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 30 8 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322311
X-RAY DIFFRACTIONf_angle_d0.57233142
X-RAY DIFFRACTIONf_chiral_restr0.036391
X-RAY DIFFRACTIONf_plane_restr0.0038367
X-RAY DIFFRACTIONf_dihedral_angle_d12.6719889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.720.40821280.3952506X-RAY DIFFRACTION98.32
2.72-2.990.39041140.34772585X-RAY DIFFRACTION99.3
2.99-3.430.31731340.3032593X-RAY DIFFRACTION99.31
3.43-4.320.27691360.25082613X-RAY DIFFRACTION99.67
4.32-58.920.24421550.2372730X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: 5.24747034401 Å / Origin y: -9.52308686296 Å / Origin z: -21.764864318 Å
111213212223313233
T0.422965376199 Å2-0.00349065742423 Å20.0492292114266 Å2-0.387407492772 Å2-0.0319037762482 Å2--0.267438556942 Å2
L1.4343787294 °2-0.425466901141 °20.117296711732 °2-3.12692335073 °2-0.58765813625 °2--1.22840332865 °2
S0.0412310861875 Å °-0.0162611921963 Å °0.124578815237 Å °-0.0165259682405 Å °-0.0268002516755 Å °-0.105281381404 Å °0.174475715609 Å °0.0236423051223 Å °-0.0247899033578 Å °
Refinement TLS groupSelection details: all

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