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

ID or keywords:

Entry

Database: PDB / ID: 24ge

Title

Crystal structure of HpsK from Ruegeria pomeroyi in complex with S-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 / (2~{S})-2,3-bis(oxidanyl)propane-1-sulfonic acid / Dihydroxypropanesulfonate (DHPS) TRAP transporter

Function and homology information

Biological species

Ruegeria pomeroyi DSS-3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 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	24ge.cif.gz	92.9 KB	Display	PDBx/mmCIF format
PDB format	pdb24ge.ent.gz	64.5 KB	Display	PDB format
PDBx/mmJSON format	24ge.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/24ge ftp://data.pdbj.org/pub/pdb/validation_reports/4g/24ge	HTTPS FTP

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Related structure data

Related structure data	24gcC 24gdC 24gfC 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

36.8 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)	84.793, 68.756, 71.377
Angle α, β, γ (deg.)	90.000, 120.323, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-680- 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-LLQ / (2~{S})-2,3-bis(oxidanyl)propane-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-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₂O₃ / Comment: precipitant*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.47 Å³/Da / Density % sol: 50.19 %
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: Oct 5, 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: 1.65→42.208 Å / Num. obs: 42559 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC_1/2: 1 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.65→1.68 Å / Num. unique obs: 2071 / CC_1/2: 1

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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: 1.65→42.208 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.964 / SU B: 1.424 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1639	2150	5.052 %	RANDOM
R_work	0.1406	40409	-	-
all	0.142	-	-	-
obs	-	42559	99.887 %	-

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: 12.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.284 Å²	0 Å²	-0.417 Å²
2-	-	0.722 Å²	-0 Å²
3-	-	-	-0.307 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→42.208 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2461	0	21	423	2905

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	2649
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2463
X-RAY DIFFRACTION	r_angle_refined_deg	1.498	1.798	3615
X-RAY DIFFRACTION	r_angle_other_deg	0.534	1.738	5675
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.367	5	350
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.184	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.824	10	416
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.416	10	119
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	390
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3235
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	627
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	581
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	2129
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	1304
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1279
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	293
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.119	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.115	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.159	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	0.882	1.228	1352
X-RAY DIFFRACTION	r_mcbond_other	0.88	1.228	1352
X-RAY DIFFRACTION	r_mcangle_it	1.319	2.211	1706
X-RAY DIFFRACTION	r_mcangle_other	1.322	2.211	1707
X-RAY DIFFRACTION	r_scbond_it	1.725	1.394	1297
X-RAY DIFFRACTION	r_scbond_other	1.724	1.396	1298
X-RAY DIFFRACTION	r_scangle_it	2.703	2.468	1905
X-RAY DIFFRACTION	r_scangle_other	2.702	2.469	1906
X-RAY DIFFRACTION	r_lrange_it	4.341	13.58	3205
X-RAY DIFFRACTION	r_lrange_other	3.999	11.785	3059

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
1.65-1.693	0.184	157	0.171	2956	0.172	3115	0.977	0.982	99.9358	0.154
1.693-1.739	0.219	169	0.168	2866	0.171	3037	0.971	0.982	99.9341	0.148
1.739-1.789	0.197	131	0.164	2837	0.166	2969	0.976	0.984	99.9663	0.145
1.789-1.844	0.164	127	0.154	2752	0.154	2881	0.984	0.986	99.9306	0.134
1.844-1.905	0.193	144	0.145	2664	0.147	2809	0.981	0.987	99.9644	0.127
1.905-1.971	0.183	145	0.148	2588	0.15	2733	0.979	0.986	100	0.132
1.971-2.046	0.178	128	0.143	2451	0.144	2579	0.981	0.988	100	0.13
2.046-2.129	0.193	136	0.141	2376	0.144	2518	0.976	0.988	99.7617	0.129
2.129-2.223	0.176	117	0.133	2319	0.135	2437	0.981	0.989	99.959	0.122
2.223-2.332	0.163	99	0.125	2172	0.127	2273	0.984	0.99	99.912	0.115
2.332-2.457	0.144	112	0.119	2135	0.12	2247	0.988	0.991	100	0.11
2.457-2.606	0.133	108	0.117	1966	0.117	2079	0.989	0.992	99.7595	0.108
2.606-2.785	0.175	108	0.129	1826	0.132	1937	0.982	0.99	99.8451	0.121
2.785-3.007	0.147	106	0.146	1744	0.146	1852	0.987	0.987	99.892	0.138
3.007-3.292	0.176	85	0.158	1595	0.158	1682	0.98	0.987	99.8811	0.153
3.292-3.678	0.198	66	0.146	1457	0.149	1526	0.98	0.989	99.8034	0.145
3.678-4.242	0.137	72	0.129	1276	0.129	1352	0.99	0.99	99.7041	0.128
4.242-5.182	0.105	58	0.125	1080	0.124	1143	0.995	0.993	99.5626	0.125
5.182-7.274	0.164	53	0.157	848	0.157	903	0.987	0.989	99.7785	0.156
7.274-42.208	0.147	29	0.152	501	0.151	532	0.989	0.983	99.6241	0.15

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