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- PDB-9l2h: Crystal structure of AnAChE N267D mutant in complex with paraoxon -

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Basic information

Entry
Database: PDB / ID: 9l2h
TitleCrystal structure of AnAChE N267D mutant in complex with paraoxon
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 / DIETHYL HYDROGEN PHOSPHATE / Cellulose-binding GDSL lipase/acylhydrolase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,6243
Polymers32,3781
Non-polymers2462
Water6,413356
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)78.722, 78.722, 91.659
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-408-

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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-DPF / DIETHYL HYDROGEN PHOSPHATE


Mass: 154.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 51.22 %
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: 1.7→68.18 Å / Num. obs: 36327 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 18.62 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.186 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1859 / CC1/2: 0.919 / % possible all: 99.1

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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: 1.71→68.18 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1674 1878 5.18 %RANDOM
Rwork0.1452 ---
obs0.1464 36285 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→68.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 6 356 2477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132229
X-RAY DIFFRACTIONf_angle_d1.2523056
X-RAY DIFFRACTIONf_dihedral_angle_d5.713313
X-RAY DIFFRACTIONf_chiral_restr0.077324
X-RAY DIFFRACTIONf_plane_restr0.01399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.21581470.162607X-RAY DIFFRACTION99
1.75-1.80.19041160.14962620X-RAY DIFFRACTION100
1.8-1.860.21121320.17812611X-RAY DIFFRACTION100
1.86-1.930.22581400.17722616X-RAY DIFFRACTION100
1.93-20.19681730.14292593X-RAY DIFFRACTION100
2-2.10.15691550.13532592X-RAY DIFFRACTION100
2.1-2.210.15991500.13782633X-RAY DIFFRACTION100
2.21-2.340.17611420.15062648X-RAY DIFFRACTION100
2.34-2.530.17841470.14012651X-RAY DIFFRACTION100
2.53-2.780.15511170.14982679X-RAY DIFFRACTION100
2.78-3.180.16261580.14452643X-RAY DIFFRACTION100
3.18-4.010.14361460.1342706X-RAY DIFFRACTION100
4.01-68.180.1611550.14522808X-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)
12.16780.29131.0861.1876-0.39971.3713-0.06790.05320.00950.0018-0.008-0.07750.01980.03480.0670.1345-0.0043-0.00950.1242-0.01010.1493-6.5269-31.411-8.3919
20.4834-0.09750.07090.70980.09430.83460.02840.0197-0.01780.0346-0.0021-0.03890.02350.0148-0.0210.1265-0.0112-0.00720.14-0.00150.1408-7.9108-28.6563-8.8753
34.0583-0.84050.49161.41820.20040.9104-0.03260.03870.2289-0.0297-0.0074-0.0468-0.20150.01510.06280.187-0.00840.01940.14010.03240.1547-9.6854-13.2844-15.3534
42.17430.46530.54991.00080.32810.99180.0301-0.01460.0139-0.0246-0.08770.0915-0.0151-0.11620.01420.1312-0.0019-0.01410.1514-0.00850.1214-18.7597-26.8613-18.3508
54.37730.6432-0.01881.17960.19951.11850.06380.28050.0634-0.1167-0.09810.0871-0.1028-0.05520.05370.18670.0347-0.02070.16760.0080.1431-18.3109-18.5815-23.4488
60.97640.30450.40910.95330.29111.10920.06020.0132-0.1568-0.0825-0.0710.10080.1341-0.19890.00840.152-0.0023-0.02190.1734-0.01380.1572-20.7513-36.212-20.9605
73.16171.28950.24791.92210.09041.65580.01030.3038-0.112-0.13720.0487-0.13610.11270.0863-0.03650.17160.0155-0.00830.1598-0.01990.146-8.165-37.1968-22.28
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 172 )
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 224 )
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 272 )
7X-RAY DIFFRACTION7chain 'A' and (resid 273 through 293 )

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