PDB-9l39: Crystal structure of AnAChE N267D-I139D mutant

ID or keywords:

Entry

Database: PDB / ID: 9l39

Title

Crystal structure of AnAChE N267D-I139D mutant

Components

Cellulose-binding GDSL lipase/acylhydrolase

Keywords

HYDROLASE / Acetylcholinesterase / SGNH hydrolase / GDSL family / Ser34-His270-Asp267 catalytic triad

Function / homology

: / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / Cellulose-binding GDSL lipase/acylhydrolase

Function and homology information

Biological species

Aspergillus niger (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.49 Å

Authors

Xing, S.Q. / Hu, G.L. / He, L.P.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Heterologous expression of a novel acetylcholinesterase from the fungus Aspergillus niger GZUF36: identification, determination of the catalytic triad, kinetic analysis, crystallization, ...
Authors: Xing, S.Q. / Hu, G.L. / Xie, W. / Wang, L. / Tian, G.H. / Yuan, Y. / Gao, F.L. / Wang, X. / Li, C.Q. / He, L.P.

History

Deposition	Dec 17, 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	9l39.cif.gz	129.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9l39.ent.gz	99.3 KB	Display	PDB format
PDBx/mmJSON format	9l39.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9l39_validation.pdf.gz	415.7 KB	Display	wwPDB validaton report
Full document	9l39_full_validation.pdf.gz	415.8 KB	Display
Data in XML	9l39_validation.xml.gz	17.6 KB	Display
Data in CIF	9l39_validation.cif.gz	26.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l3/9l39 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/9l39	HTTPS FTP

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Related structure data

Related structure data	9l1rSC 9l1tC 9l27C 9l2aC 9l2bC 9l2cC 9l2hC 9l2jC 9l2mC 9l2pC 9l34C 9l37C 9l3aC 9l3bC S: Starting model for refinement 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	#54 - Jun 2004 Acetylcholinesterase similarity (1)

Deposited unit

A: Cellulose-binding GDSL lipase/acylhydrolase

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	79.207, 79.207, 91.906
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-520- HOH

#1: Protein	Cellulose-binding GDSL lipase/acylhydrolase / acetylcholinesterase (AnAChE) Mass: 32379.750 Da / Num. of mol.: 1 / Mutation: N267D,I139D Source method: isolated from a genetically manipulated source Details: GenBank: ULM60884.1 / Source: (gene. exp.) Aspergillus niger (mold) / Strain: GZUF36 / Gene: CAN33_0018055 / Plasmid: pGEX4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A254UBZ6, acetylcholinesterase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52.14 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.0 M Ammonium sulfate, 0.1 M Tris(hydroxymethyl)aminomethane-HCl, pH 8.5 PH range: 8-9

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 1.49→45.95 Å / Num. obs: 55327 / % possible obs: 100 % / Redundancy: 19 % / B_iso Wilson estimate: 18.92 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.054 / Net I/σ(I): 31.4
Reflection shell	Resolution: 1.49→1.51 Å / Redundancy: 15.8 % / R_merge(I) obs: 0.842 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2692 / CC_1/2: 0.849 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS	Jan 10, 2022	data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	4.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 9L1R

9l1r

Resolution: 1.49→39.6 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1569	2703	4.89 %
R_work	0.1424	-	-
obs	0.1431	55271	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.49→39.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2107	0	0	391	2498

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2233
X-RAY DIFFRACTION	f_angle_d	1.139	3066
X-RAY DIFFRACTION	f_dihedral_angle_d	5.449	314
X-RAY DIFFRACTION	f_chiral_restr	0.096	325
X-RAY DIFFRACTION	f_plane_restr	0.01	405

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 (%)
1.49-1.51	0.2038	136	0.2092	2723	X-RAY DIFFRACTION	100
1.51-1.54	0.1965	127	0.1755	2757	X-RAY DIFFRACTION	100
1.54-1.57	0.2224	143	0.163	2731	X-RAY DIFFRACTION	100
1.57-1.61	0.1718	141	0.1515	2732	X-RAY DIFFRACTION	100
1.61-1.65	0.1861	131	0.1473	2745	X-RAY DIFFRACTION	100
1.65-1.69	0.1788	127	0.1436	2774	X-RAY DIFFRACTION	100
1.69-1.73	0.1929	165	0.148	2724	X-RAY DIFFRACTION	100
1.73-1.78	0.1897	108	0.1481	2744	X-RAY DIFFRACTION	100
1.78-1.84	0.195	133	0.1577	2761	X-RAY DIFFRACTION	100
1.84-1.91	0.1988	155	0.1545	2739	X-RAY DIFFRACTION	100
1.91-1.98	0.1845	160	0.1389	2732	X-RAY DIFFRACTION	100
1.98-2.07	0.155	135	0.1346	2737	X-RAY DIFFRACTION	100
2.07-2.18	0.1526	144	0.1347	2765	X-RAY DIFFRACTION	100
2.18-2.32	0.1638	133	0.1413	2786	X-RAY DIFFRACTION	100
2.32-2.5	0.1704	134	0.1369	2794	X-RAY DIFFRACTION	100
2.5-2.75	0.1619	133	0.1485	2802	X-RAY DIFFRACTION	100
2.75-3.15	0.155	191	0.1444	2745	X-RAY DIFFRACTION	100
3.15-3.97	0.1369	162	0.13	2819	X-RAY DIFFRACTION	100
3.97-39.6	0.1274	145	0.1408	2958	X-RAY DIFFRACTION	100

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	2.2947	0.6224	-0.9056	1.8682	0.5792	1.9408	-0.0226	0.0453	0.0652	0.0399	-0.0096	0.0539	-0.0314	-0.0647	0.0279	0.1284	-0.0021	0.0105	0.1174	0.0181	0.1262	5.8873	31.6893	-9.1909
2	0.7041	-0.2049	-0.1186	0.6231	-0.1133	0.7388	0.0133	0.0411	0.0727	0.0625	0.0291	0.0629	-0.0892	-0.0619	-0.0422	0.1576	-0.0079	0.0141	0.166	0.002	0.1622	8.5912	33.8266	-8.1052
3	1.7415	-0.1526	-0.356	0.9829	-0.0508	1.0681	0.0052	0.0236	-0.0533	0.0603	-0.035	0.0531	0.0648	-0.0488	0.0235	0.1533	-0.0209	-0.0035	0.146	-0.0084	0.1355	7.0158	22.5388	-9.434
4	4.0578	-1.2032	-0.7928	1.5061	0.1999	0.9729	-0.0188	0.1428	-0.2796	-0.0503	-0.0233	0.1032	0.1821	-0.1031	0.0886	0.1953	-0.0256	-0.0092	0.171	-0.0311	0.1722	9.2658	13.3606	-15.4495
5	2.8739	0.7341	-0.8127	1.1828	-0.3013	1.0957	0.0175	-0.0424	-0.1124	-0.0562	-0.0719	-0.1041	0.0472	0.0642	0.0582	0.1444	0.0086	0.0141	0.1692	0.0151	0.1329	18.881	27.0129	-18.4185
6	8.6429	0.682	0.4885	1.5154	0.1315	1.1729	0.0655	0.4459	-0.0708	-0.1612	-0.1	-0.0261	0.1523	-0.0441	0.0416	0.2146	0.027	0.0241	0.2013	-0.0042	0.1534	18.3086	18.5216	-23.5967
7	3.5448	1.1003	-0.3514	1.321	-0.5037	0.8979	0.0238	0.2635	0.0494	-0.1259	-0.0294	-0.0339	0.0223	-0.1013	0.0091	0.1842	0.0113	0.013	0.2048	-0.0021	0.125	13.5472	29.4842	-25.6468
8	0.9771	-0.1244	-0.2634	1.2465	-0.4889	1.8564	0.0799	-0.0138	0.1777	-0.06	-0.0867	-0.1712	-0.1344	0.234	-0.0001	0.1883	-0.0314	0.017	0.2308	0.0332	0.2597	25.6947	41.1188	-17.8633
9	4.5302	1.8799	-0.2005	2.8492	-0.011	2.1561	0.0364	0.3371	0.1312	-0.1841	0.0193	0.1729	-0.0784	-0.1852	-0.0332	0.1849	0.0293	0.0093	0.2001	0.0282	0.1558	8.1819	37.4234	-22.3436

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 105 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 150 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 151 through 172 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 173 through 195 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 196 through 224 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 225 through 243 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 244 through 272 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 273 through 293 )

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