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- PDB-9l2b: Crystal structure of AnAChE in complex with carbaryl -

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Basic information

Entry
Database: PDB / ID: 9l2b
TitleCrystal structure of AnAChE in complex with carbaryl
ComponentsCellulose-binding GDSL lipase/acylhydrolase
KeywordsHYDROLASE / Acetylcholinesterase / SGNH hydrolase / GDSL family / Ser34-His270-Asn267 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 speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 16, 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


Theoretical massNumber of molelcules
Total (without water)32,4341
Polymers32,4341
Non-polymers00
Water7,440413
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)79.347, 79.347, 92.827
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-439-

HOH

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Components

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


Mass: 32433.891 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting 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: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.49→55.23 Å / Num. obs: 55336 / % possible obs: 98.6 % / Redundancy: 18 % / CC1/2: 0.998 / Net I/σ(I): 17.1
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 8119 / CC1/2: 0.861 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSJan 10, 2022data reduction
Aimlessdata scaling
PHASESphasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→28.21 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1654 2831 5.12 %
Rwork0.1431 --
obs0.1442 55279 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 0 413 2524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112240
X-RAY DIFFRACTIONf_angle_d1.2033074
X-RAY DIFFRACTIONf_dihedral_angle_d5.564317
X-RAY DIFFRACTIONf_chiral_restr0.098327
X-RAY DIFFRACTIONf_plane_restr0.01404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.21161400.20082641X-RAY DIFFRACTION100
1.51-1.540.23111630.18552596X-RAY DIFFRACTION100
1.54-1.570.21211490.17482638X-RAY DIFFRACTION100
1.57-1.60.20241590.16052626X-RAY DIFFRACTION100
1.6-1.640.1611410.15462601X-RAY DIFFRACTION100
1.64-1.670.18661290.14842674X-RAY DIFFRACTION100
1.67-1.720.1731250.15012636X-RAY DIFFRACTION100
1.72-1.760.17531420.13792665X-RAY DIFFRACTION100
1.76-1.810.1721390.1452595X-RAY DIFFRACTION100
1.81-1.870.15821490.14512649X-RAY DIFFRACTION100
1.87-1.940.19171050.16092285X-RAY DIFFRACTION85
1.94-2.020.16631070.14142302X-RAY DIFFRACTION86
2.02-2.110.15791370.14512652X-RAY DIFFRACTION100
2.11-2.220.18351300.13712682X-RAY DIFFRACTION100
2.22-2.360.18381330.14992653X-RAY DIFFRACTION100
2.36-2.540.1671640.1492635X-RAY DIFFRACTION100
2.54-2.80.17851640.15052665X-RAY DIFFRACTION100
2.8-3.20.17351500.14282699X-RAY DIFFRACTION100
3.2-4.030.14861550.12322726X-RAY DIFFRACTION100
4.03-28.210.13321500.13642828X-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)
10.16690.0257-0.17520.15710.09910.2870.0296-0.04910.0580.0170.0367-0.0256-0.06740.138800.1546-0.00950.01140.1672-0.01470.167533.377813.38948.904
20.20260.02010.02970.130.1370.68510.0352-0.03110.0233-0.0113-0.0089-0.0142-0.05580.025700.10950.00440.00670.1245-0.00620.13428.11488.06477.5563
30.62510.1155-0.1090.1149-0.21330.9006-0.01730.0033-0.025-0.1040.01370.05640.0862-0.0394-00.14590.0019-0.00780.130.00140.140124.8741-0.8592-0.3417
40.34790.3565-0.01060.3642-0.00740.2471-0.03770.1049-0.1224-0.2358-0.01730.05760.0558-0.10220.00010.21820.001-0.00360.1583-0.0160.16725.4072-6.9002-8.1269
50.14930.0337-0.14960.41740.1270.685-0.062-0.02520.0316-0.10090.0658-0.13330.02920.18030.00450.16850.01860.02760.2113-0.00890.178942.05980.176-5.7006
60.1061-0.0439-0.14460.06570.07230.20080.02550.14650.0963-0.16930.0015-0.0497-0.15840.1149-0.00020.2025-0.0120.02040.18290.00630.177436.537611.5504-7.0521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 224 )
5X-RAY DIFFRACTION5chain 'A' and (resid 225 through 272 )
6X-RAY DIFFRACTION6chain 'A' and (resid 273 through 293 )

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