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- PDB-9l1r: Crystal structure of AnAChE in apo form, a fungal acetylcholinest... -

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Basic information

Entry
Database: PDB / ID: 9l1r
TitleCrystal structure of AnAChE in apo form, a fungal acetylcholinesterase from Aspergillus niger
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: 1.5 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 15, 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


Theoretical massNumber of molelcules
Total (without water)32,3771
Polymers32,3771
Non-polymers00
Water4,666259
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)78.957, 78.957, 91.867
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-301-

HOH

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Components

#1: Protein Cellulose-binding GDSL lipase/acylhydrolase


Mass: 32376.836 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
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: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.5→68.38 Å / Num. obs: 53854 / % possible obs: 99.7 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Rrim(I) all: 0.1 / Χ2: 0.89 / Net I/σ(I): 13
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 7704 / CC1/2: 0.841 / Rpim(I) all: 0.238 / Rrim(I) all: 0.63 / Χ2: 0.72 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PDB_EXTRACT4.1data extraction
XDSJan 10, 2022data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→68.38 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.901 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17492 2731 5.1 %RANDOM
Rwork0.14729 ---
obs0.14871 51087 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.588 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.5→68.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 0 259 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122171
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161928
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.6632966
X-RAY DIFFRACTIONr_angle_other_deg0.5971.5754462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1855270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.20456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70110323
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2751.6471077
X-RAY DIFFRACTIONr_mcbond_other1.2731.6471077
X-RAY DIFFRACTIONr_mcangle_it1.7572.9591345
X-RAY DIFFRACTIONr_mcangle_other1.7572.9591346
X-RAY DIFFRACTIONr_scbond_it2.9241.8651094
X-RAY DIFFRACTIONr_scbond_other2.9231.8651095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3123.3031621
X-RAY DIFFRACTIONr_long_range_B_refined4.94917.572589
X-RAY DIFFRACTIONr_long_range_B_other4.77716.572539
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.534 Å
RfactorNum. reflection% reflection
Rfree0.245 206 -
Rwork0.222 3652 -
obs--98.07 %

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