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

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Basic information

Entry
Database: PDB / ID: 28sv
TitleStructure of ASBT homologue from Leptospira biflexa in inward-facing form (Crystal Form 1)
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 / FORMIC ACID / (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: 2.21 Å
AuthorsGrob, A. / 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.
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
B: Putative transporter, sodium/bile acid transporter family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,71929
Polymers66,3692
Non-polymers7,35027
Water1,67593
1
A: Putative transporter, sodium/bile acid transporter family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,80812
Polymers33,1851
Non-polymers2,62311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative transporter, sodium/bile acid transporter family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,91217
Polymers33,1851
Non-polymers4,72716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.583, 94.902, 107.602
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

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Protein , 1 types, 2 molecules AB

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


Mass: 33184.570 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 120 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.19 %
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% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.21→56 Å / Num. obs: 34241 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 33 Å2 / CC1/2: 0.466 / CC star: 0.797 / Rmerge(I) obs: 0.2404 / Rpim(I) all: 0.1069 / Net I/σ(I): 6.13
Reflection shellResolution: 2.21→2.28 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.621 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 2770 / CC1/2: 0.403 / CC star: 0.758 / Rpim(I) all: 0.7837 / Rrim(I) all: 1.804 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→56 Å / SU ML: 0.2482 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 1658 4.85 %
Rwork0.1782 32528 -
obs0.1806 34186 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.61 Å2
Refinement stepCycle: LAST / Resolution: 2.21→56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 379 93 4956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01264931
X-RAY DIFFRACTIONf_angle_d1.31566566
X-RAY DIFFRACTIONf_chiral_restr0.0556778
X-RAY DIFFRACTIONf_plane_restr0.0092765
X-RAY DIFFRACTIONf_dihedral_angle_d19.66791935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.280.28921190.24072632X-RAY DIFFRACTION98.81
2.28-2.350.29011500.22592664X-RAY DIFFRACTION99.75
2.35-2.430.29821190.21632707X-RAY DIFFRACTION99.93
2.43-2.530.25431270.19442675X-RAY DIFFRACTION99.75
2.53-2.650.26511590.18052653X-RAY DIFFRACTION100
2.65-2.790.21451430.18012671X-RAY DIFFRACTION99.89
2.79-2.960.22561270.17462714X-RAY DIFFRACTION99.86
2.96-3.190.22591350.16692712X-RAY DIFFRACTION99.96
3.19-3.510.20761420.16662718X-RAY DIFFRACTION100
3.51-4.020.21461550.16392709X-RAY DIFFRACTION100
4.02-5.060.20241320.15842795X-RAY DIFFRACTION100
5.06-560.22351500.18712878X-RAY DIFFRACTION99.61
Refinement TLS params.Method: refined / Origin x: 6.13561755224 Å / Origin y: -1.40842282602 Å / Origin z: -31.8243514288 Å
111213212223313233
T0.20681393446 Å20.00385130081889 Å20.0095180497261 Å2-0.184055473945 Å20.00568115813053 Å2--0.21443718669 Å2
L0.570219768115 °20.0273422595845 °20.493408271671 °2-0.348660684908 °2-0.0338800203322 °2--1.23805940145 °2
S0.0354815613888 Å °-0.01824440828 Å °-0.0280143590224 Å °0.0297249656168 Å °-0.00177751948619 Å °0.0207096430662 Å °0.0270982747302 Å °-0.0722258775872 Å °-0.0349864745326 Å °
Refinement TLS groupSelection details: all

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