PDB-9l2j: Crystal structure of AnAChE S34A mutant

ID or keywords:

Entry

Database: PDB / ID: 9l2j

Title

Crystal structure of AnAChE S34A mutant

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 / Cellulose-binding GDSL lipase/acylhydrolase

Function and homology information

Biological species

Aspergillus niger (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 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	9l2j.cif.gz	129.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9l2j.ent.gz	98.8 KB	Display	PDB format
PDBx/mmJSON format	9l2j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9l2j_validation.pdf.gz	431.5 KB	Display	wwPDB validaton report
Full document	9l2j_full_validation.pdf.gz	431.5 KB	Display
Data in XML	9l2j_validation.xml.gz	18.9 KB	Display
Data in CIF	9l2j_validation.cif.gz	28.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l2/9l2j ftp://data.pdbj.org/pub/pdb/validation_reports/l2/9l2j	HTTPS FTP

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Related structure data

Related structure data	9l1rC 9l1tC 9l27C 9l2aC 9l2bC 9l2cC 9l2hC 9l2mC 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

32.9 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)	77.910, 77.910, 90.107
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-541- HOH
2	1	A-651- HOH
3	1	A-755- HOH
4	1	A-793- 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.44 Å³/Da / Density % sol: 49.58 %
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: 0.97861 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: 0.97861 Å / Relative weight: 1
Reflection	Resolution: 1.5→29.47 Å / Num. obs: 50685 / % possible obs: 100 % / Redundancy: 18.9 % / B_iso Wilson estimate: 14.64 Å² / CC_1/2: 1 / R_merge(I) obs: 0.043 / Χ²: 1.04 / Net I/σ(I): 47.8
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 16.6 % / R_merge(I) obs: 0.419 / Mean I/σ(I) obs: 7 / Num. unique obs: 2490 / CC_1/2: 0.969 / Χ²: 0.91 / % 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 / Resolution: 1.5→29.47 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 16.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1679	2638	5.23 %	RANDOM
R_work	0.1463	-	-	-
obs	0.1475	50442	99.57 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 14.64 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→29.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2106	0	36	429	2571

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2260
X-RAY DIFFRACTION	f_angle_d	1.175	3098
X-RAY DIFFRACTION	f_dihedral_angle_d	8.205	339
X-RAY DIFFRACTION	f_chiral_restr	0.067	330
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 (%)
1.5-1.52	0.254	162	0.1922	3091	X-RAY DIFFRACTION	100
1.52-1.54	0.19	210	0.1568	2997	X-RAY DIFFRACTION	100
1.54-1.56	0.2032	164	0.1525	3094	X-RAY DIFFRACTION	100
1.56-1.58	0.1737	168	0.1426	3017	X-RAY DIFFRACTION	100
1.58-1.6	0.1758	176	0.1455	3085	X-RAY DIFFRACTION	100
1.6-1.62	0.19	144	0.1322	3123	X-RAY DIFFRACTION	100
1.62-1.64	0.1849	186	0.1462	3024	X-RAY DIFFRACTION	100
1.64-1.67	0.1923	176	0.1363	3103	X-RAY DIFFRACTION	100
1.67-1.69	0.1775	148	0.1337	3105	X-RAY DIFFRACTION	100
1.69-1.72	0.1374	134	0.1456	3040	X-RAY DIFFRACTION	100
1.72-1.75	0.1345	164	0.141	3089	X-RAY DIFFRACTION	100
1.75-1.78	0.167	170	0.1381	3048	X-RAY DIFFRACTION	100
1.78-1.82	0.1467	156	0.1539	3114	X-RAY DIFFRACTION	100
1.82-1.85	0.2179	180	0.1541	3087	X-RAY DIFFRACTION	100
1.85-1.9	0.1892	173	0.1576	3034	X-RAY DIFFRACTION	100
1.9-1.94	0.3248	161	0.2308	2845	X-RAY DIFFRACTION	93
1.94-1.99	0.1459	106	0.1437	3119	X-RAY DIFFRACTION	100
1.99-2.04	0.176	126	0.1378	3097	X-RAY DIFFRACTION	100
2.04-2.1	0.2024	194	0.1453	3041	X-RAY DIFFRACTION	100
2.1-2.17	0.1639	178	0.1406	3082	X-RAY DIFFRACTION	100
2.17-2.25	0.1975	222	0.1631	2948	X-RAY DIFFRACTION	98
2.25-2.34	0.1519	182	0.1569	2958	X-RAY DIFFRACTION	98
2.34-2.44	0.1546	148	0.1367	3103	X-RAY DIFFRACTION	100
2.44-2.57	0.1758	161	0.145	3043	X-RAY DIFFRACTION	100
2.57-2.73	0.1712	186	0.1569	3051	X-RAY DIFFRACTION	100
2.73-2.94	0.1637	164	0.152	3070	X-RAY DIFFRACTION	100
2.94-3.24	0.1912	172	0.1428	3101	X-RAY DIFFRACTION	100
3.24-3.71	0.1375	184	0.1255	3057	X-RAY DIFFRACTION	100
3.71-4.67	0.1172	208	0.1229	3012	X-RAY DIFFRACTION	100
4.67-29.47	0.1683	160	0.157	3084	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	2.1522	-0.7786	-0.0577	0.8223	0.9208	1.71	-0.0051	0.0083	0.0997	-0.0063	-0.026	-0.0433	-0.0511	-0.0078	0.034	0.1058	-0.0179	0.0074	0.0777	0.0076	0.0993	28.9164	10.6221	5.6229
2	0.5174	0.103	-0.0636	0.6105	0.0111	0.4797	0.0085	-0.018	0.0735	-0.0031	0.0045	-0.0333	-0.072	0.0225	-0.0149	0.1329	-0.0095	0.0006	0.1092	0.0008	0.1232	32.1662	9.27	6.7132
3	1.1877	-1.4956	-0.1901	5.2068	-0.0152	1.395	-0.0557	-0.1152	0.0091	0.1759	0.0293	0.171	-0.046	-0.0427	0.0211	0.0871	0.0021	-0.0116	0.1223	0.0013	0.0923	18.7302	10.5023	11.2776
4	0.8965	-0.5374	-0.0447	1.0951	0.11	0.3446	0.0018	0.0297	-0.0655	-0.0889	0.0021	0.0375	0.0304	-0.0791	-0.0014	0.1371	-0.0206	-0.0096	0.1251	0.0067	0.1121	23.5337	-1.6457	-0.8406
5	4.3924	-4.2057	0.8184	5.2303	-0.7493	0.8095	0.1179	0.1838	-0.0863	-0.2635	-0.1426	0.0691	0.0665	-0.0502	0.0035	0.1717	-0.038	-0.0078	0.13	-0.0112	0.1097	23.7797	-6.7624	-8.4138
6	1.236	-0.4257	-0.0928	0.7457	0.102	0.6075	-0.0115	0.1125	0.0404	-0.084	0.0041	-0.1449	-0.0288	0.0442	0.0141	0.1545	-0.0291	0.0169	0.1143	0.0031	0.1362	38.778	3.5483	-6.3386

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 195 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 196 through 224 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 225 through 293 )

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