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- PDB-9l2c: Crystal structure of AnAChE N267D mutant in complex with acetate -

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Basic information

Entry
Database: PDB / ID: 9l2c
TitleCrystal structure of AnAChE N267D mutant in complex with acetate
ComponentsCellulose-binding GDSL lipase/acylhydrolase
KeywordsHYDROLASE / 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 / ACETATE ION / Cellulose-binding GDSL lipase/acylhydrolase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsXing, S.Q. / Hu, G.L. / He, L.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870002 China
CitationJournal: 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, ...Title: Heterologous expression of a novel acetylcholinesterase from the fungus Aspergillus niger GZUF36: identification, determination of the catalytic triad, kinetic analysis, crystallization, crystal structure of the ligand complex, catalytic mechanism, and analysis of its mechanism for acylated choline specificity
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
DepositionDec 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose-binding GDSL lipase/acylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6214
Polymers32,3781
Non-polymers2433
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.628, 78.628, 91.351
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

#1: Protein Cellulose-binding GDSL lipase/acylhydrolase / AnAChE


Mass: 32377.820 Da / Num. of mol.: 1 / Mutation: N267D
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: isolated from a natural source / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.79→68.09 Å / Num. obs: 31522 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 17.77 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.175 / Net I/σ(I): 12.8
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1795 / CC1/2: 0.939 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSJan 10, 2022data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→68.09 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 1518 4.82 %RANDOM
Rwork0.145 ---
obs0.1467 31481 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→68.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 16 417 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162228
X-RAY DIFFRACTIONf_angle_d1.3523052
X-RAY DIFFRACTIONf_dihedral_angle_d6.837314
X-RAY DIFFRACTIONf_chiral_restr0.084324
X-RAY DIFFRACTIONf_plane_restr0.012400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.30091520.24222664X-RAY DIFFRACTION100
1.84-1.910.22631430.18982706X-RAY DIFFRACTION100
1.91-1.990.18681430.14092650X-RAY DIFFRACTION100
1.99-2.080.14361300.13042720X-RAY DIFFRACTION100
2.08-2.190.18391280.14122699X-RAY DIFFRACTION100
2.19-2.320.19381650.15352669X-RAY DIFFRACTION100
2.32-2.50.20781490.13882688X-RAY DIFFRACTION100
2.5-2.750.1691500.14412715X-RAY DIFFRACTION100
2.75-3.150.1991160.14112777X-RAY DIFFRACTION100
3.15-3.970.13771210.12822767X-RAY DIFFRACTION100
3.97-68.090.18051210.14412908X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
12.1552-2.10230.24863.5372-0.40270.75640.06390.1662-0.0721-0.311-0.09280.03790.064-0.07580.0270.1808-0.0170.00080.1636-0.02510.139224.7154-6.2295-8.2601
20.8646-0.0142-0.30390.57730.12160.8477-0.00610.05230.0065-0.13230.016-0.11440.00370.1027-0.00350.14770.00210.02090.1425-0.00580.141639.90093.6806-6.0984
31.2626-0.2011-0.30930.7250.911.16070.0208-0.00320.05420.01-0.02760.047-0.0264-0.04040.01960.11160.00290.00810.1235-0.00430.132530.253410.47946.0995
40.4990.0944-0.05790.5609-0.04230.55780.0371-0.02120.0612-0.0226-0.0385-0.0207-0.07570.005-0.0050.12670.00410.0060.1378-0.01120.132629.76319.81818.3633
50.5964-0.1044-0.15861.0514-0.02580.6899-0.01010.034-0.024-0.1272-0.00780.03250.0585-0.05710.01090.12420.0063-0.00970.1272-0.00840.111424.6117-1.2675-0.6095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 196 through 224 )
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 42 )
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 195 )

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