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- PDB-24gg: Crystal structure of apo HpsK from Bilophila wadsworthia -

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Basic information

Entry
Database: PDB / ID: 24gg
TitleCrystal structure of apo HpsK from Bilophila wadsworthia
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 / DctP family TRAP transporter solute receptor
Function and homology information
Biological speciesBilophila wadsworthia 3_1_6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,4572
Polymers69,4572
Non-polymers00
Water7,368409
1
A: DctP family TRAP transporter solute receptor


Theoretical massNumber of molelcules
Total (without water)34,7291
Polymers34,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DctP family TRAP transporter solute receptor


Theoretical massNumber of molelcules
Total (without water)34,7291
Polymers34,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.017, 87.806, 65.954
Angle α, β, γ (deg.)90.000, 108.841, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DctP family TRAP transporter solute receptor


Mass: 34728.621 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Tris, pH 8.5, 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: 0.954 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: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.01→48.41 Å / Num. obs: 39014 / % possible obs: 98.2 % / Redundancy: 7.1 % / CC1/2: 0.99 / Net I/σ(I): 6.6
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 2772 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.006→35.936 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.671 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1989 5.101 %RANDOM
Rwork0.1747 37004 --
all0.177 ---
obs-38993 97.995 %-
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: 21.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.244 Å2-0 Å2-0.757 Å2
2--1.379 Å2-0 Å2
3----0.898 Å2
Refinement stepCycle: LAST / Resolution: 2.006→35.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4867 0 0 409 5276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125030
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164817
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.8076841
X-RAY DIFFRACTIONr_angle_other_deg0.51.76811098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.357522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00210862
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.52410230
X-RAY DIFFRACTIONr_chiral_restr0.0690.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021152
X-RAY DIFFRACTIONr_nbd_refined0.2170.21109
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.24374
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22481
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2362
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.211
X-RAY DIFFRACTIONr_nbd_other0.1770.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.29
X-RAY DIFFRACTIONr_mcbond_it1.4242.0772480
X-RAY DIFFRACTIONr_mcbond_other1.4242.0772480
X-RAY DIFFRACTIONr_mcangle_it2.1273.7253100
X-RAY DIFFRACTIONr_mcangle_other2.1273.7263101
X-RAY DIFFRACTIONr_scbond_it2.3682.3972550
X-RAY DIFFRACTIONr_scbond_other2.3682.3972551
X-RAY DIFFRACTIONr_scangle_it3.8484.2493734
X-RAY DIFFRACTIONr_scangle_other3.8474.2493735
X-RAY DIFFRACTIONr_lrange_it4.74321.1875954
X-RAY DIFFRACTIONr_lrange_other4.70820.4545870
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
2.006-2.0580.3111320.26326290.26529450.9360.95293.75210.254
2.058-2.1140.2851380.23426300.23728400.9430.96497.46480.225
2.114-2.1760.2551280.21725540.21827470.9580.9797.63380.205
2.176-2.2420.2571360.21224920.21526900.9520.9797.69520.197
2.242-2.3150.2541340.20224210.20526110.9580.97397.85520.189
2.315-2.3960.2531300.18423600.18725410.9610.97997.99290.167
2.396-2.4860.2411250.17222490.17624200.9650.98298.09920.156
2.486-2.5870.2171160.17921930.18123520.9740.98198.17180.16
2.587-2.7020.2471170.16820790.17322310.970.98398.43120.15
2.702-2.8330.2521110.17820400.18221830.9580.98198.53410.16
2.833-2.9850.238960.17719150.1820380.9620.9898.67520.162
2.985-3.1650.2341030.19218280.19419520.9570.97798.92420.181
3.165-3.3810.237920.17817140.18118280.9680.98298.79650.171
3.381-3.650.224950.16516090.16817170.9680.98599.24290.162
3.65-3.9940.187740.14614720.14815640.980.98898.84910.145
3.994-4.4580.182720.12513310.12814120.9830.99299.36260.129
4.458-5.1350.174550.13512160.13712780.9880.99399.45230.141
5.135-6.2570.188630.15210040.15410730.9830.9999.44080.155
6.257-8.7180.194410.1338000.1358450.9860.99199.52660.139
8.718-35.9360.217310.1824680.1855060.9870.98998.61660.193

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