PDB-9k8u: Ethanol dehydrogenase of Bursaphelenchus xylophilus

ID or keywords:

Entry

Database: PDB / ID: 9k8u

Title

Ethanol dehydrogenase of Bursaphelenchus xylophilus

Components

alcohol dehydrogenase

Keywords

OXIDOREDUCTASE / Alcohol dehydrogenase / zinc-type

Function / homology

Function and homology information

alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding / cytoplasm
Similarity search - Function

Biological species

Bursaphelenchus xylophilus (pine wood nematode)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.81 Å

Authors

Xing, Z.F. / Luo, X. / Li, X.Y. / Song, R.J. / Song, B.A.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Ethanol dehydrogenase of Bursaphelenchus xylophilus
Authors: Xing, Z.F.

History

Deposition	Oct 24, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9k8u.cif.gz	536.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9k8u.ent.gz	446.1 KB	Display	PDB format
PDBx/mmJSON format	9k8u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9k8u_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	9k8u_full_validation.pdf.gz	3.3 MB	Display
Data in XML	9k8u_validation.xml.gz	58.4 KB	Display
Data in CIF	9k8u_validation.cif.gz	75.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k8/9k8u ftp://data.pdbj.org/pub/pdb/validation_reports/k8/9k8u	HTTPS FTP

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Related structure data

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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (11) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: alcohol dehydrogenase

B: alcohol dehydrogenase

C: alcohol dehydrogenase

D: alcohol dehydrogenase

hetero molecules

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

1

A: alcohol dehydrogenase

D: alcohol dehydrogenase

hetero molecules

B: alcohol dehydrogenase

C: alcohol dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration
150 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.707, 152.773, 63.792
Angle α, β, γ (deg.)	90.00, 95.73, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	alcohol dehydrogenase Mass: 37485.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bursaphelenchus xylophilus (pine wood nematode) Gene: BXYJ_LOCUS12742 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A1I7RMX2, alcohol dehydrogenase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 2.09 Å³/Da / Density % sol: 41.27 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Dilithium sulfate 0.1M Hepes 0.1M PH7.5 PEG3350 25% PH range: 7.2-7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.81→45.48 Å / Num. obs: 29682 / % possible obs: 98.8 % / Redundancy: 6.34 % / R_rim(I) all: 0.184 / Net I/σ(I): 7.55
Reflection shell	Resolution: 2.81→2.98 Å / R_merge(I) obs: 1.725 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 4676

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHENIX	1.20.1_4487	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.81→43.1 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2984	1488	5.02 %
R_work	0.2577	-	-
obs	0.2597	29641	98.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.81→43.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10496	0	8	0	10504

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10696
X-RAY DIFFRACTION	f_angle_d	1.048	14499
X-RAY DIFFRACTION	f_dihedral_angle_d	12.615	3892
X-RAY DIFFRACTION	f_chiral_restr	0.063	1679
X-RAY DIFFRACTION	f_plane_restr	0.01	1872

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 (%)
2.81-2.9	0.4056	134	0.3718	2439	X-RAY DIFFRACTION	95
2.9-3	0.3639	129	0.3138	2576	X-RAY DIFFRACTION	100
3-3.13	0.3178	135	0.3145	2562	X-RAY DIFFRACTION	99
3.13-3.27	0.3588	139	0.3138	2558	X-RAY DIFFRACTION	99
3.27-3.44	0.3269	142	0.2888	2577	X-RAY DIFFRACTION	99
3.44-3.65	0.3483	136	0.2668	2561	X-RAY DIFFRACTION	100
3.65-3.94	0.3227	136	0.2641	2579	X-RAY DIFFRACTION	99
3.94-4.33	0.2668	131	0.2399	2564	X-RAY DIFFRACTION	99
4.33-4.96	0.264	137	0.2186	2561	X-RAY DIFFRACTION	99
4.96-6.24	0.316	134	0.2636	2595	X-RAY DIFFRACTION	100
6.25-43.1	0.2478	135	0.2295	2581	X-RAY DIFFRACTION	98

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	2.9607	-1.0583	0.0405	1.8205	0.6125	3.2805	0.4383	-0.1092	-0.0302	-0.169	0.0421	0.5176	0.0471	0.0227	-0.4917	0.6331	0.0057	-0.0342	0.5636	0.1689	0.9112	-28.3516	46.0831	-24.591
2	1.9027	0.3731	-1.1276	2.2402	-2.6825	2.3344	0.1497	-0.3651	-0.0102	-0.1689	0.0779	0.3559	0.226	-0.0187	-0.0998	0.5967	0.0145	0.0012	0.4981	0.0753	0.7932	-24.9543	34.9408	-17.0441
3	2.0309	-0.2834	-0.8738	2.8553	1.7427	-0.8205	0.1225	0.2639	0.176	-0.1193	-0.0445	-0.0353	-0.1233	-0.0564	-0.0813	0.6728	0.0998	-0.0321	0.6035	0.1452	0.5548	-21.5433	25.2834	-27.7323
4	3.6073	-1.6616	1.226	2.0013	-0.8671	3.9306	0.5364	1.3659	-0.3586	-0.6132	0.0574	0.2216	0.015	0.1704	-0.3792	0.6908	-0.0913	-0.0601	1.0514	0.0432	0.7247	-30.9747	10.259	-39.7826
5	2.9061	0.3416	0.177	0.8315	-1.6415	3.3876	0.0444	0.6784	0.0306	-0.1263	0.1573	0.4437	-0.1481	-0.4627	-0.171	0.3686	0.0342	-0.025	0.6468	0.0622	0.4474	-33.7567	7.2425	-23.571
6	1.7932	-0.3675	0.4542	2.367	-0.3207	2.2386	0.0001	0.2838	-0.3967	-0.1333	0.0252	0.651	-0.1145	-0.0935	0.0233	0.6083	-0.0144	0.0982	0.7317	0.0681	0.7521	-26.4335	31.6351	-33.8167
7	1.1037	-0.021	-0.5088	0.7536	0.6694	0.6545	0.8114	0.225	1.0572	0.8357	-0.6374	-0.5083	-1.0335	0.2746	-0.1877	1.467	-0.1541	0.1641	0.7189	0.0336	1.3696	2.1144	39.5156	10.3312
8	2.9283	-0.1879	-1.0539	1.8968	-0.9155	5.4234	0.2574	0.4546	-0.1096	0.6093	-0.0506	-0.042	-1.1135	0.3151	-0.304	0.8534	-0.0166	0.0421	0.5067	-0.0877	0.6407	-2.2594	31.6988	-0.4962
9	2.2936	-0.086	0.0444	4.3566	-0.5081	2.2446	0.0307	-0.1902	-0.042	0.429	0.1228	0.2757	-0.3575	0.3078	-0.1257	0.5794	0.0623	0.0141	0.5326	-0.0182	0.331	-3.1621	13.1206	8.3798
10	3.2927	-0.4305	-0.2733	1.2243	-1.4961	2.6404	-0.0281	-0.2192	0.2357	-0.0682	-0.3825	-0.3323	0.2827	0.6553	0.3015	0.4563	0.0229	-0.0173	0.5287	0.0498	0.3587	5.5167	3.4237	-3.5544
11	5.2342	1.2577	0.108	2.4935	0.6486	1.9122	0.1124	-0.4888	-0.116	0.423	0.0319	-0.474	-1.1798	0.7204	-0.2044	0.9469	-0.2059	-0.0189	0.9679	-0.0281	0.4794	-0.8226	22.7674	14.1368
12	2.1389	0.7383	0.5818	2.5079	-1.0522	2.8809	0.0596	-0.0165	-0.0805	0.1785	0.1898	-0.0258	0.4066	0.1232	-0.0975	0.7224	0.0188	0.1	0.4084	-0.1564	0.7693	3.6577	-25.1557	-33.0819
13	4.7262	-0.1391	1.7083	1.8018	0.7479	1.8923	-0.6516	-0.3281	-0.625	0.3488	0.621	-0.3379	-0.4568	0.0203	0.0582	0.7672	0.1473	0.0853	0.4753	-0.0106	0.4855	6.5477	-17.4698	-26.2628
14	1.9455	0.571	0.3424	1.2089	1.7205	1.7254	-0.1077	0.028	-0.1559	-0.4131	-0.19	0.4884	-0.1385	-0.14	0.2508	0.5225	0.0442	-0.088	0.4418	-0.0769	0.5329	-5.9825	-13.7725	-26.1852
15	2.6286	-0.6362	1.4278	2.4845	-0.2346	3.6103	-0.0454	0.4774	0.0765	0.0538	0.2686	-0.35	-0.2733	0.9647	-0.1167	0.3738	-0.052	-0.0161	0.5853	-0.0677	0.3835	5.4537	12.9946	-28.3214
16	2.5057	0.2014	0.6016	3.7054	2.1494	2.8329	0.034	0.0692	-0.3023	-0.0312	0.0229	-0.3738	-0.061	0.6081	-0.1263	0.3391	-0.0148	-0.0379	0.7493	0.027	0.4751	6.8122	6.5006	-14.2725
17	2.767	-1.5184	-0.9915	2.9137	0.311	2.1852	-0.2133	-0.0815	0.1333	0.0485	-0.0425	-0.2024	0.1438	0.0829	0.2319	0.5771	-0.0073	0.0089	0.5939	-0.0321	0.5313	3.1933	-8.4387	-36.9446
18	1.2067	0.2852	0.6195	-0.1552	0.6336	-0.2082	0.8049	-0.1382	0.017	-0.656	-0.0798	0.4218	0.1279	-0.5411	-0.8222	1.4416	0.0515	0.0718	0.8619	0.3555	1.8716	-32.5962	-29.6128	-5.9822
19	2.2169	-0.5806	-0.1157	2.3597	-1.2059	2.2617	0.1866	0.0414	-0.5564	0.0997	0.1721	1.292	0.4827	-0.1896	-0.1998	0.806	-0.0705	-0.0059	0.637	0.11	1.2498	-26.1008	-19.2942	-10.0206
20	2.2491	-1.1954	-0.7657	2.462	2.5747	1.673	-0.4396	-0.1584	-0.1083	-0.1424	0.1927	0.1154	0.3377	0.091	0.1361	0.5033	0.0677	0.1224	0.5655	0.2255	0.7354	-26.2523	-1.2458	1.7124
21	2.4753	2.0104	-1.083	1.9058	-0.1859	2.3833	0.8773	-0.6027	0.5624	0.4785	-0.857	0.4861	-0.6444	-0.3933	-0.1117	0.9825	0.132	0.2143	0.9028	-0.0534	0.661	-36.5235	7.2483	10.1839
22	2.7393	0.5057	-1.6695	2.2354	-0.6418	2.4816	-0.3059	-0.1297	-0.7281	0.4567	0.467	0.2768	-0.0511	-0.1736	-0.1276	0.45	0.0741	-0.0214	0.512	0.0336	0.6163	-32.2078	2.8041	-3.1008
23	3.9779	0.9725	-0.1995	1.4999	2.1073	3.4391	-0.5671	1.501	0.9155	0.9092	0.5936	-0.096	-0.3001	-1.0532	-0.802	1.4163	0.1027	0.6652	1.3756	0.5542	2.8895	-40.3838	-17.8656	4.6425

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 43 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 121 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 122 through 193 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 194 through 226 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 227 through 297 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 298 through 347 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 43 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 44 through 121 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 122 through 226 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 227 through 297 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 298 through 347 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 43 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 44 through 76 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 77 through 165 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 166 through 267 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 268 through 297 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 298 through 347 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1 through 43 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 44 through 145 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 146 through 194 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 195 through 226 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 227 through 326 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 327 through 346 )

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