PDB-9l2m: Crystal structure of AnAChE S34A mutant in complex with acetate

ID or keywords:

Entry

Database: PDB / ID: 9l2m

Title

Crystal structure of AnAChE S34A mutant in complex with acetate

Components

Cellulose-binding GDSL lipase/acylhydrolase

Keywords

HYDROLASE / Acetylcholinesterase / SGNH hydrolase / GDSL family / S34A

Function / homology

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

Function and homology information

Biological species

Aspergillus niger (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 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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PDBx/mmCIF format	9l2m.cif.gz	127.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9l2m.ent.gz	97.4 KB	Display	PDB format
PDBx/mmJSON format	9l2m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9l2m_validation.pdf.gz	703 KB	Display	wwPDB validaton report
Full document	9l2m_full_validation.pdf.gz	702.9 KB	Display
Data in XML	9l2m_validation.xml.gz	17.5 KB	Display
Data in CIF	9l2m_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l2/9l2m ftp://data.pdbj.org/pub/pdb/validation_reports/l2/9l2m	HTTPS FTP

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Related structure data

Related structure data	9l1rC 9l1tC 9l27C 9l2aC 9l2bC 9l2cC 9l2hC 9l2jC 9l2pC 9l34C 9l37C 9l39C 9l3aC 9l3bC 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

hetero molecules

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)	78.826, 78.826, 91.406
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-410- HOH

#1: Protein	Cellulose-binding GDSL lipase/acylhydrolase / AnAChE Mass: 32360.836 Da / Num. of mol.: 1 / Mutation: S34A Source method: isolated from a genetically manipulated source Details: NCBI accession number 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: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.53 Å³/Da / Density % sol: 51.45 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M Ammonium sulfate, 10%(v/v) 1,4-dioxane, 0.1 M 2-Morpholinoethanesulphonic acid, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97907 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97907 Å / Relative weight: 1
Reflection	Resolution: 1.53→68.27 Å / Num. obs: 50457 / % possible obs: 100 % / Redundancy: 19.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.083 / Net I/σ(I): 21
Reflection shell	Resolution: 1.53→1.55 Å / Redundancy: 18 % / R_merge(I) obs: 0.916 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2466 / CC_1/2: 0.885 / % possible all: 100

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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 / Resolution: 1.53→68.27 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1723	2638	5.23 %
R_work	0.1515	-	-
obs	0.1526	50411	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.53→68.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2106	0	4	358	2468

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	2222
X-RAY DIFFRACTION	f_angle_d	1.245	3049
X-RAY DIFFRACTION	f_dihedral_angle_d	5.748	312
X-RAY DIFFRACTION	f_chiral_restr	0.077	325
X-RAY DIFFRACTION	f_plane_restr	0.012	401

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 (%)
1.53-1.55	0.2768	128	0.1958	2486	X-RAY DIFFRACTION	100
1.55-1.58	0.2077	154	0.1687	2456	X-RAY DIFFRACTION	100
1.58-1.62	0.184	137	0.1626	2478	X-RAY DIFFRACTION	100
1.62-1.65	0.1768	126	0.1524	2513	X-RAY DIFFRACTION	100
1.65-1.69	0.1793	138	0.1523	2467	X-RAY DIFFRACTION	100
1.69-1.73	0.168	126	0.1545	2501	X-RAY DIFFRACTION	100
1.73-1.78	0.2093	126	0.1779	2514	X-RAY DIFFRACTION	100
1.78-1.83	0.234	125	0.1874	2505	X-RAY DIFFRACTION	100
1.83-1.89	0.1947	151	0.1653	2477	X-RAY DIFFRACTION	100
1.89-1.96	0.1706	139	0.1469	2503	X-RAY DIFFRACTION	100
1.96-2.04	0.199	101	0.1391	2531	X-RAY DIFFRACTION	100
2.04-2.13	0.1777	145	0.1446	2510	X-RAY DIFFRACTION	100
2.13-2.24	0.1672	145	0.1571	2497	X-RAY DIFFRACTION	100
2.24-2.38	0.1732	171	0.1463	2481	X-RAY DIFFRACTION	100
2.38-2.56	0.1694	139	0.1471	2529	X-RAY DIFFRACTION	100
2.56-2.82	0.1736	139	0.156	2533	X-RAY DIFFRACTION	100
2.82-3.23	0.1937	143	0.1528	2528	X-RAY DIFFRACTION	100
3.23-4.07	0.1464	151	0.1387	2587	X-RAY DIFFRACTION	100
4.07-68.27	0.1535	154	0.1507	2677	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	1.9885	-0.2703	0.2985	1.2015	-1.1245	1.7479	0.0288	-0.0159	-0.0704	-0.0358	-0.0388	-0.0376	0.0481	0.0194	0.0321	0.1444	0.0039	-0.0106	0.151	0.0099	0.1669	-30.1578	-10.8757	6.0245
2	0.3667	0.0295	0.0485	0.7528	-0.0431	0.6058	0.0588	-0.0249	-0.0764	0.0045	-0.0192	0.0254	0.0727	-0.0457	-0.0287	0.153	0.004	-0.0104	0.1703	0.0126	0.1711	-33.4409	-9.5056	7.0835
3	0.6343	-0.4915	0.1076	2.4815	0.1261	0.9731	0.0075	-0.1346	-0.1046	0.0767	-0.0415	-0.075	0.1453	0.0862	-0.0042	0.1276	0.0098	0.0103	0.1748	0.0184	0.1549	-19.952	-10.5416	11.6792
4	0.7769	-0.0655	0.2026	2.2191	-0.187	1.1363	-0.0186	0.0062	0.0145	-0.1249	0.0152	-0.0457	-0.0327	0.0569	0.0123	0.1326	0.0044	0.0081	0.157	0.001	0.1389	-25.377	-0.9282	1.1671
5	1.2013	-0.5489	0.2385	3.5795	-0.191	1.0755	-0.0082	0.0618	-0.0059	0.0279	-0.0161	-0.1519	-0.09	0.1919	0.0309	0.1643	-0.0068	0.0317	0.2083	0.0053	0.1847	-16.1185	1.1128	0.1945
6	1.6117	-0.7229	0.5675	1.5911	-0.276	1.0688	-0.0095	0.007	0.0557	-0.1282	-0.0305	0.06	-0.0705	-0.0205	0.0311	0.1579	0.0031	-0.0053	0.1513	0.0148	0.1411	-32.6373	2.876	-3.0655
7	3.2665	-2.7735	-0.2524	4.5735	0.5291	0.88	0.0739	0.1732	0.0897	-0.3373	-0.1061	-0.0747	-0.0538	0.0993	0.0228	0.2407	-0.0155	0.0068	0.1997	0.0313	0.1748	-24.7629	6.2688	-8.2535
8	0.7226	-0.0243	0.3039	0.7655	-0.1579	1.1475	-0.0287	0.0096	0.0197	-0.1152	0.0215	0.1475	-0.0725	-0.1688	0.011	0.1879	0.013	-0.0291	0.1746	0.0035	0.1846	-41.722	-0.1252	-5.6531
9	2.577	-1.1563	0.3031	1.9884	-0.0965	1.5382	0.0599	0.235	-0.1328	-0.2727	-0.045	0.0334	0.1475	0.0011	-0.0412	0.2146	-0.0079	-0.023	0.1811	-0.0012	0.1707	-36.2837	-11.4764	-7.1486

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 124 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 150 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 151 through 172 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 173 through 195 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 196 through 224 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 225 through 272 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 273 through 293 )

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