PDB-9x6i: Crystal structure of L-threonate 3-dehydrogenase from Paracoccus ...

ID or keywords:

Entry

Database: PDB / ID: 9x6i

Title

Crystal structure of L-threonate 3-dehydrogenase from Paracoccus litorisediminis (ligand-free form)

Components

SDR family NAD(P)-dependent oxidoreductase

Keywords

OXIDOREDUCTASE / short chain dehydrogenase /reductase superfamily

Function / homology

short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / DI(HYDROXYETHYL)ETHER / SDR family NAD(P)-dependent oxidoreductase

Function and homology information

Biological species

Paracoccus litorisediminis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Watanabe, S. / Sato, H.

Funding support

1items

Citation

Journal: J.Biol.Chem. / Year: 2026
Title: Identification, functional characterization, and structural analysis of an atypical l-threonate 3-dehydrogenase.
Authors: Watanabe, S. / Sato, H. / Yokoi, T. / Terawaki, S.I.

History

Deposition	Oct 15, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 18, 2026	Provider: repository / Type: Initial release
Revision 1.1	Mar 25, 2026	Group: Structure summary / Category: struct / Item: _struct.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9x6i.cif.gz	1 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x6/9x6i ftp://data.pdbj.org/pub/pdb/validation_reports/x6/9x6i	HTTPS FTP

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Related structure data

Related structure data	9xaxC 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	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (3) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

Deposited unit

A: SDR family NAD(P)-dependent oxidoreductase

B: SDR family NAD(P)-dependent oxidoreductase

C: SDR family NAD(P)-dependent oxidoreductase

D: SDR family NAD(P)-dependent oxidoreductase

E: SDR family NAD(P)-dependent oxidoreductase

F: SDR family NAD(P)-dependent oxidoreductase

G: SDR family NAD(P)-dependent oxidoreductase

H: SDR family NAD(P)-dependent oxidoreductase

I: SDR family NAD(P)-dependent oxidoreductase

J: SDR family NAD(P)-dependent oxidoreductase

K: SDR family NAD(P)-dependent oxidoreductase

L: SDR family NAD(P)-dependent oxidoreductase

hetero molecules

332 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SDR family NAD(P)-dependent oxidoreductase

B: SDR family NAD(P)-dependent oxidoreductase

E: SDR family NAD(P)-dependent oxidoreductase

F: SDR family NAD(P)-dependent oxidoreductase

hetero molecules

defined by author
111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: SDR family NAD(P)-dependent oxidoreductase

G: SDR family NAD(P)-dependent oxidoreductase

J: SDR family NAD(P)-dependent oxidoreductase

hetero molecules

I: SDR family NAD(P)-dependent oxidoreductase

hetero molecules

defined by author
110 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: SDR family NAD(P)-dependent oxidoreductase

H: SDR family NAD(P)-dependent oxidoreductase

hetero molecules

K: SDR family NAD(P)-dependent oxidoreductase

hetero molecules

L: SDR family NAD(P)-dependent oxidoreductase

hetero molecules

defined by author
110 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.763, 73.454, 141.288
Angle α, β, γ (deg.)	83.15, 80.76, 83.81
Int Tables number	1
Space group name H-M	P1

#1: Protein	SDR family NAD(P)-dependent oxidoreductase Mass: 27366.127 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus litorisediminis (bacteria) / Gene: GL300_07955 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A844HLS7
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1826 / 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: 2.15 Å³/Da / Density % sol: 42.84 %
Crystal grow	Temperature: 293 K / Method: evaporation Details: 0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→48.29 Å / Num. obs: 211315 / % possible obs: 97.9 % / Redundancy: 7.27 % / CC_1/2: 0.999 / Net I/σ(I): 19.3
Reflection shell	Resolution: 1.9→1.93 Å / Num. unique obs: 10418 / CC_1/2: 0.716

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
PDB_EXTRACT		data extraction
XDS		data scaling
PHASER		phasing
Coot		model building
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→47.74 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 20.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1993	10435	4.94 %
R_work	0.1685	-	-
obs	0.1701	211235	97.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→47.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20706	0	196	1826	22728

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	21258
X-RAY DIFFRACTION	f_angle_d	0.942	29032
X-RAY DIFFRACTION	f_dihedral_angle_d	11.526	7390
X-RAY DIFFRACTION	f_chiral_restr	0.061	3439
X-RAY DIFFRACTION	f_plane_restr	0.008	3805

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.92	0.2658	356	0.2364	6619	X-RAY DIFFRACTION	97
1.92-1.94	0.2594	323	0.2348	6651	X-RAY DIFFRACTION	97
1.94-1.97	0.2492	320	0.2222	6596	X-RAY DIFFRACTION	97
1.97-1.99	0.2607	334	0.2125	6727	X-RAY DIFFRACTION	97
1.99-2.02	0.2507	357	0.1998	6535	X-RAY DIFFRACTION	97
2.02-2.05	0.2336	346	0.1997	6672	X-RAY DIFFRACTION	97
2.05-2.08	0.2418	356	0.1963	6617	X-RAY DIFFRACTION	97
2.08-2.11	0.2511	377	0.1919	6616	X-RAY DIFFRACTION	97
2.11-2.14	0.2238	362	0.1866	6626	X-RAY DIFFRACTION	97
2.14-2.17	0.2402	339	0.1872	6673	X-RAY DIFFRACTION	97
2.17-2.21	0.2099	369	0.1746	6607	X-RAY DIFFRACTION	98
2.21-2.25	0.2226	328	0.164	6693	X-RAY DIFFRACTION	98
2.25-2.3	0.2119	309	0.1664	6713	X-RAY DIFFRACTION	98
2.3-2.34	0.2068	354	0.1682	6642	X-RAY DIFFRACTION	98
2.34-2.39	0.1973	343	0.1675	6761	X-RAY DIFFRACTION	98
2.39-2.45	0.2155	324	0.1709	6712	X-RAY DIFFRACTION	98
2.45-2.51	0.2126	345	0.167	6688	X-RAY DIFFRACTION	98
2.51-2.58	0.2166	334	0.1716	6742	X-RAY DIFFRACTION	98
2.58-2.65	0.2035	316	0.1689	6738	X-RAY DIFFRACTION	98
2.65-2.74	0.2019	354	0.1723	6733	X-RAY DIFFRACTION	98
2.74-2.84	0.2077	379	0.1759	6694	X-RAY DIFFRACTION	99
2.84-2.95	0.2283	366	0.1723	6702	X-RAY DIFFRACTION	98
2.95-3.09	0.2043	299	0.1713	6775	X-RAY DIFFRACTION	98
3.09-3.25	0.2192	362	0.1729	6684	X-RAY DIFFRACTION	98
3.25-3.45	0.1866	375	0.1649	6740	X-RAY DIFFRACTION	98
3.45-3.72	0.1774	359	0.1515	6733	X-RAY DIFFRACTION	99
3.72-4.09	0.1726	372	0.15	6785	X-RAY DIFFRACTION	99
4.09-4.68	0.1512	362	0.1341	6773	X-RAY DIFFRACTION	99
4.68-5.9	0.1654	372	0.1555	6762	X-RAY DIFFRACTION	99
5.9-47.74	0.1931	343	0.1768	6791	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.6661	-0.2067	0.4261	1.0359	-0.3158	1.046	-0.0179	-0.0826	0.0393	0.1278	-0.0207	0.0871	-0.3055	-0.0558	0.0388	0.2053	-0.0138	-0.0002	0.1759	-0.0278	0.1277	0.7989	-0.4484	-0.2886
2	0.7209	-0.0812	0.1043	1.302	-0.1131	1.3253	0.0321	0.1585	-0.1609	-0.163	-0.0192	-0.0004	0.0659	0.1113	-0.0142	0.115	-0.0027	-0.024	0.1906	-0.0405	0.1592	9.7979	-24.2937	-14.5716
3	1.0993	-0.0081	-0.0151	1.0035	0.0713	1.814	-0.1005	-0.0899	0.0585	0.187	0.0942	-0.0751	0.1149	0.1046	0.0031	0.1603	0.031	-0.0284	0.1102	0.0019	0.1611	12.5013	-22.9064	61.8696
4	0.8035	-0.2003	0.1047	1.238	0.136	0.8105	0.0718	0.0716	0.1205	0.1264	0.0364	-0.1694	-0.4125	0.0199	-0.0896	0.2905	0.0217	0.0209	0.1328	0.025	0.2076	-11.6936	14.9069	-38.0383
5	0.3991	0.0557	0.1087	0.1817	-0.0925	0.1049	0.0132	-0.032	0.1092	0.119	-0.0548	-0.1593	-0.3868	0.3552	0.016	0.3417	-0.1851	-0.0542	0.3567	0.0048	0.2234	27.6788	2.6325	11.2772
6	0.7455	0.2637	-0.1874	0.4756	0.0136	0.1381	0.0575	0.0142	-0.1548	0.0485	-0.0229	-0.2123	0.0572	0.4564	-0.0294	0.1503	0.0066	-0.0367	0.4719	0.0117	0.2737	34.5752	-24.2211	1.4814
7	1.1831	-0.0688	0.0852	0.6362	0.2402	0.7816	-0.0334	0.235	0.2005	-0.081	-0.0037	0.1584	-0.2562	-0.4709	0.0425	0.2044	0.0537	-0.0357	0.3522	0.0599	0.2589	-6.9278	-12.7907	42.1818
8	0.57	-0.1111	-0.3968	1.4706	0.375	1.7875	-0.054	0.1421	-0.2149	0.1363	0.0447	0.0927	0.2707	-0.1727	0.0109	0.1436	-0.0034	-0.0167	0.1796	-0.0217	0.2474	-21.0377	-12.1519	-44.7523
9	0.4017	0.2796	0.0775	0.7327	-0.4199	0.4681	-0.1019	0.0853	-0.1837	0.0667	0.0398	-0.0795	0.6836	0.094	0.0327	0.5643	0.0244	0.0636	0.1745	-0.0153	0.2587	20.8012	24.3533	47.4792
10	0.3096	-0.0573	-0.1685	0.1142	0.0369	0.1002	-0.1103	0.2548	-0.1358	-0.0401	-0.0535	0.3101	0.4389	-0.5213	0.0406	0.371	-0.2773	0.0253	0.5213	-0.0858	0.3351	-9.812	-40.2589	31.8127
11	0.1032	-0.0976	-0.0944	0.2103	-0.0369	0.2046	0.2201	0.2144	0.2072	0.0087	-0.0069	0.2621	-0.4185	-0.3932	-0.0975	0.4772	0.5902	0.213	0.4047	0.2707	0.4031	23.2925	-47.7388	-44.4395
12	0.2402	-0.1368	-0.2599	0.3234	-0.0547	0.4785	0.0239	0.4139	-0.1508	-0.2031	-0.0138	0.4689	0.0094	-0.674	-0.072	0.1499	0.0678	-0.095	0.9247	0.004	0.4718	24.4487	-0.0719	-56.2342

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H
9	X-RAY DIFFRACTION	9	chain I
10	X-RAY DIFFRACTION	10	chain J
11	X-RAY DIFFRACTION	11	chain K
12	X-RAY DIFFRACTION	12	chain L

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