PDB-24gf: Crystal structure of HpsK from Ruegeria pomeroyi in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 24gf

Title

Crystal structure of HpsK from Ruegeria pomeroyi in complex with R-DHPS (2,3-dihydroxypropanesulfonate)

Components

Dihydroxypropanesulfonate (DHPS) TRAP transporter

Keywords

PROTEIN BINDING / solute binding protein

Function / homology

TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / transmembrane transport / periplasmic space / : / Dihydroxypropanesulfonate (DHPS) TRAP transporter

Function and homology information

Biological species

Ruegeria pomeroyi DSS-3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.958 Å

Authors

Lee, M.

Funding support

Australia, 1items

Citation

Journal: 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

Deposition	Mar 3, 2026	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 26, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	24gf.cif.gz	88 KB	Display	PDBx/mmCIF format
PDB format	pdb24gf.ent.gz		Display	PDB format
PDBx/mmJSON format	24gf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/4g/24gf ftp://data.pdbj.org/pub/pdb/validation_reports/4g/24gf	HTTPS FTP

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Related structure data

Related structure data	24gcC 24gdC 24geC 24ggC 24ghC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#220 - Apr 2018 Dehalogenases similarity (2) #111 - Mar 2009 Hydrogenase similarity (2)

Deposited unit

A: Dihydroxypropanesulfonate (DHPS) TRAP transporter

hetero molecules

36.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	84.791, 69.464, 71.473
Angle α, β, γ (deg.)	90.000, 120.420, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-697- HOH

#1: Protein	Dihydroxypropanesulfonate (DHPS) TRAP transporter / HpsK Mass: 36364.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) / Gene: hpsK, SPO0591 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5LVV4
#2: Chemical	ChemComp-A1AZH / (2R)-2,3-dihydroxypropane-1-sulfonic acid Mass: 156.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, BIS-TRIS, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 1.96→48.07 Å / Num. obs: 25729 / % possible obs: 99.7 % / Redundancy: 3.5 % / CC_1/2: 1 / Net I/σ(I): 12.1
Reflection shell	Resolution: 1.96→2.01 Å / Num. unique obs: 1747 / CC_1/2: 0.93

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0431	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.958→42.218 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.949 / SU B: 2.754 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1779	1218	4.734 %	RANDOM
R_work	0.1439	24511	-	-
all	0.146	-	-	-
obs	-	25729	99.605 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 14.476 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.234 Å²	-0 Å²	-0.527 Å²
2-	-	0.892 Å²	-0 Å²
3-	-	-	-0.024 Å²

Refinement step

Cycle: LAST / Resolution: 1.958→42.218 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2461	0	12	316	2789

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	2565
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2391
X-RAY DIFFRACTION	r_angle_refined_deg	1.427	1.792	3493
X-RAY DIFFRACTION	r_angle_other_deg	0.504	1.735	5498
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.402	5	334
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.08	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.526	10	399
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.409	10	114
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	381
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3095
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	607
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	564
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	2146
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1279
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	1252
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	235
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.032	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.097	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.197	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	0.999	1.445	1312
X-RAY DIFFRACTION	r_mcbond_other	0.998	1.444	1312
X-RAY DIFFRACTION	r_mcangle_it	1.513	2.591	1642
X-RAY DIFFRACTION	r_mcangle_other	1.515	2.591	1643
X-RAY DIFFRACTION	r_scbond_it	1.981	1.639	1253
X-RAY DIFFRACTION	r_scbond_other	1.982	1.64	1251
X-RAY DIFFRACTION	r_scangle_it	3.168	2.909	1847
X-RAY DIFFRACTION	r_scangle_other	3.167	2.908	1848
X-RAY DIFFRACTION	r_lrange_it	4.745	14.675	3054
X-RAY DIFFRACTION	r_lrange_other	4.52	13.678	2969

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.958-2.009	0.207	84	0.189	1745	0.19	1851	0.976	0.979	98.8115	0.17
2.009-2.064	0.204	76	0.156	1781	0.158	1859	0.975	0.985	99.8924	0.139
2.064-2.124	0.191	73	0.147	1743	0.149	1822	0.979	0.987	99.6707	0.13
2.124-2.189	0.173	94	0.139	1640	0.141	1734	0.98	0.988	100	0.121
2.189-2.26	0.17	82	0.138	1606	0.14	1691	0.983	0.988	99.8226	0.12
2.26-2.34	0.189	60	0.133	1574	0.135	1637	0.979	0.99	99.8167	0.116
2.34-2.428	0.178	72	0.126	1497	0.128	1569	0.981	0.99	100	0.111
2.428-2.526	0.165	80	0.129	1466	0.131	1547	0.985	0.99	99.9354	0.115
2.526-2.638	0.192	71	0.133	1396	0.136	1468	0.977	0.989	99.9319	0.12
2.638-2.766	0.2	72	0.138	1317	0.141	1391	0.975	0.989	99.8562	0.127
2.766-2.915	0.187	73	0.146	1261	0.149	1337	0.979	0.988	99.7756	0.133
2.915-3.091	0.181	65	0.155	1195	0.156	1264	0.98	0.986	99.6835	0.144
3.091-3.304	0.224	56	0.166	1127	0.168	1185	0.969	0.985	99.8312	0.158
3.304-3.566	0.173	60	0.169	1045	0.17	1114	0.987	0.986	99.1921	0.166
3.566-3.904	0.19	44	0.147	989	0.149	1037	0.983	0.989	99.6143	0.146
3.904-4.36	0.124	58	0.121	845	0.121	909	0.991	0.992	99.3399	0.124
4.36-5.026	0.161	38	0.121	788	0.123	833	0.99	0.993	99.1597	0.124
5.026-6.134	0.191	26	0.14	668	0.142	697	0.986	0.992	99.5696	0.14
6.134-8.584	0.162	23	0.141	518	0.142	550	0.982	0.99	98.3636	0.146
8.584-42.218	0.147	11	0.156	310	0.156	326	0.986	0.984	98.4663	0.168

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