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- PDB-24gh: Crystal structure of HpsK from Bilophila wadsworthia in complex w... -

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Basic information

Entry
Database: PDB / ID: 24gh
TitleCrystal structure of HpsK from Bilophila wadsworthia in complex with S-DHPS (2,3-dihydroxypropanesulfonate)
ComponentsDctP family TRAP transporter solute receptor
KeywordsPROTEIN BINDING / solute binding protein
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / (2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid / DctP family TRAP transporter solute receptor
Function and homology information
Biological speciesBilophila wadsworthia 3_1_6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsLee, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chem Sci / Year: 2026
Title: Chiral recognition of 2,3-dihydroxypropanesulfonate by bacterial transport proteins adapted to distinct ecological niches.
Authors: Barber, H. / Borusak, S. / Stewart, A.W.E. / Tahir, H. / Scott, N.E. / Schleheck, D. / Lee, M. / Williams, S.J.
History
DepositionMar 3, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DctP family TRAP transporter solute receptor
B: DctP family TRAP transporter solute receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8136
Polymers73,4302
Non-polymers3834
Water15,439857
1
A: DctP family TRAP transporter solute receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9424
Polymers36,7151
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area13810 Å2
MethodPISA
2
B: DctP family TRAP transporter solute receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8712
Polymers36,7151
Non-polymers1561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.753, 52.048, 66.644
Angle α, β, γ (deg.)70.309, 88.754, 80.142
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DctP family TRAP transporter solute receptor


Mass: 36714.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bilophila wadsworthia 3_1_6 (bacteria) / Gene: HMPREF0179_02146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5Y7I1
#2: Chemical ChemComp-LLQ / (2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid


Mass: 156.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Bis-Tris, pH 5.5, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.827 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.05→46.659 Å / Num. obs: 285217 / % possible obs: 94.7 % / Redundancy: 3.6 % / CC1/2: 1 / Net I/σ(I): 11.3
Reflection shellResolution: 1.05→1.07 Å / Num. unique obs: 13723 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→46.659 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.661 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1361 14616 5.125 %RANDOM
Rwork0.1178 270600 --
all0.119 ---
obs-285216 94.724 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.197 Å2
Baniso -1Baniso -2Baniso -3
1-0.181 Å20.139 Å2-0.104 Å2
2--0.067 Å2-0.088 Å2
3----0.208 Å2
Refinement stepCycle: LAST / Resolution: 1.05→46.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 20 857 5858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125613
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165371
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.8257674
X-RAY DIFFRACTIONr_angle_other_deg0.6741.78212429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.406527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12110997
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1710255
X-RAY DIFFRACTIONr_chiral_restr0.1090.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026882
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021302
X-RAY DIFFRACTIONr_nbd_refined0.2530.21259
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.24798
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22755
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2565
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2680.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.30.211
X-RAY DIFFRACTIONr_nbd_other0.2610.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.245
X-RAY DIFFRACTIONr_mcbond_it3.2211.0342773
X-RAY DIFFRACTIONr_mcbond_other3.2051.0342773
X-RAY DIFFRACTIONr_mcangle_it4.431.8643545
X-RAY DIFFRACTIONr_mcangle_other4.4391.8653546
X-RAY DIFFRACTIONr_scbond_it5.3281.2552840
X-RAY DIFFRACTIONr_scbond_other5.3291.2562838
X-RAY DIFFRACTIONr_scangle_it7.4352.2014129
X-RAY DIFFRACTIONr_scangle_other7.4352.2014130
X-RAY DIFFRACTIONr_lrange_it12.10814.6366902
X-RAY DIFFRACTIONr_lrange_other9.85311.1476597
X-RAY DIFFRACTIONr_rigid_bond_restr4.196310984
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.05-1.0770.19310380.186195040.186223720.9790.98291.82010.172
1.077-1.1070.16210010.158190100.158216900.9860.98692.25910.141
1.107-1.1390.1499930.133185560.134210640.9880.9992.80760.116
1.139-1.1740.1319530.115181620.115205600.990.99292.97180.098
1.174-1.2120.1279460.106175890.107198520.990.99393.36590.091
1.212-1.2550.1259320.099170940.101191850.9910.99493.95880.086
1.255-1.3020.1168840.094166660.095185960.9920.99594.37510.081
1.302-1.3550.118240.09160200.091177930.9930.99594.66640.079
1.355-1.4160.1158650.089154420.09171240.9920.99595.22890.079
1.416-1.4850.1118730.085147520.086163580.9920.99695.5190.077
1.485-1.5650.1067830.082141140.083155330.9940.99695.90550.077
1.565-1.660.1067130.083134520.085147180.9940.99696.24270.08
1.66-1.7740.1186710.092127310.093138530.9920.99596.74440.09
1.774-1.9160.136310.102118580.103128920.990.99496.8740.103
1.916-2.0980.1356100.115108280.116118080.990.99396.86650.12
2.098-2.3460.135310.11498550.114107060.990.99297.0110.124
2.346-2.7070.1434530.12287050.12394210.9880.99197.20840.14
2.707-3.3130.1544470.1473580.1479880.9850.98897.70910.164
3.313-4.6730.1443110.14157410.14161840.9880.98997.86550.173
4.673-46.6590.2191570.19631630.19734030.9820.98697.5610.246

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