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- PDB-9l27: Crystal structure of AnAChE in complex with acetate -

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Basic information

Entry
Database: PDB / ID: 9l27
TitleCrystal structure of AnAChE in complex with acetate
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 / ACETATE ION / Cellulose-binding GDSL lipase/acylhydrolase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5283
Polymers32,3771
Non-polymers1512
Water8,359464
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)78.625, 78.625, 91.536
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-403-

HOH

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Components

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


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 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 51.24 %
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: 1.48→50 Å / Num. obs: 55325 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 38.85
Reflection shellResolution: 1.48→1.52 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 5.93 / Num. unique obs: 4062 / CC1/2: 0.915 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACT4.1data extraction
XDSJan 10, 2022data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→39.31 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1507 2702 4.9 %RANDOM
Rwork0.1341 ---
obs0.135 55168 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.81 Å2
Refinement stepCycle: LAST / Resolution: 1.48→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2107 0 10 464 2581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012249
X-RAY DIFFRACTIONf_angle_d1.2063088
X-RAY DIFFRACTIONf_dihedral_angle_d5.849321
X-RAY DIFFRACTIONf_chiral_restr0.093328
X-RAY DIFFRACTIONf_plane_restr0.011407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.20811300.18532715X-RAY DIFFRACTION98
1.5-1.530.18311340.16962701X-RAY DIFFRACTION99
1.53-1.560.20781400.15122728X-RAY DIFFRACTION100
1.56-1.60.17551420.14112723X-RAY DIFFRACTION100
1.6-1.640.16361290.13472736X-RAY DIFFRACTION99
1.64-1.680.16461230.13342770X-RAY DIFFRACTION100
1.68-1.720.16521720.13072716X-RAY DIFFRACTION100
1.72-1.770.16171050.13712731X-RAY DIFFRACTION100
1.77-1.830.1841350.14522784X-RAY DIFFRACTION100
1.83-1.890.18971530.1422722X-RAY DIFFRACTION100
1.89-1.970.17011600.13252727X-RAY DIFFRACTION100
1.97-2.060.13831350.12632749X-RAY DIFFRACTION100
2.06-2.170.13961460.12622764X-RAY DIFFRACTION100
2.17-2.30.1491330.13042791X-RAY DIFFRACTION100
2.3-2.480.15031340.13012781X-RAY DIFFRACTION100
2.48-2.730.15841330.13892805X-RAY DIFFRACTION100
2.73-3.130.14991930.13472745X-RAY DIFFRACTION100
3.13-3.940.13031600.12182826X-RAY DIFFRACTION100
3.94-39.310.13211450.13572952X-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)
13.1929-0.44030.04761.9483-1.38542.55730.0261-0.0007-0.0811-0.0233-0.0413-0.0070.0348-0.00980.06110.0556-0.009-0.02290.0762-0.00010.0749-30.451-10.21676.2767
20.43150.07990.15050.6014-0.02190.59190.018-0.0033-0.0134-0.0597-0.0153-0.00180.00640.013-0.00210.08460.01060.00360.09640.00370.0918-27.2644-4.52744.0581
36.2734-5.6666-0.55075.25190.50040.46810.16420.21250.0598-0.4045-0.1694-0.0695-0.050.077-0.02340.1732-0.00750.00590.1380.01720.1367-24.55156.0143-8.3481
41.6995-0.42270.44940.9201-0.20480.8991-0.01350.0379-0.0244-0.12230.01490.12520.0097-0.0970.00110.1222-0.005-0.02180.1210.00520.1042-39.7885-3.9103-6.1972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 195 )
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 224 )
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 293 )

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