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- PDB-9l3a: Crystal structure of AnAChE N267D-Y102W mutant -

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Basic information

Entry
Database: PDB / ID: 9l3a
TitleCrystal structure of AnAChE N267D-Y102W mutant
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 / Cellulose-binding GDSL lipase/acylhydrolase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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


Theoretical massNumber of molelcules
Total (without water)32,4011
Polymers32,4011
Non-polymers00
Water5,098283
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)79.041, 79.041, 91.553
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-331-

HOH

21A-509-

HOH

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Components

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


Mass: 32400.855 Da / Num. of mol.: 1 / Mutation: N267D,Y102W
Source method: isolated from a genetically manipulated source
Details: GenBank: 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.: 283 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.73 %
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: Nov 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.06→45.78 Å / Num. obs: 20478 / % possible obs: 97.3 % / Redundancy: 15.1 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 25.5
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1166 / CC1/2: 0.566 / % possible all: 73.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9L1R

9l1r


Resolution: 2.06→39.52 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 1080 5.29 %
Rwork0.1569 --
obs0.1586 20421 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 283 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042176
X-RAY DIFFRACTIONf_angle_d0.6952975
X-RAY DIFFRACTIONf_dihedral_angle_d5.365292
X-RAY DIFFRACTIONf_chiral_restr0.046316
X-RAY DIFFRACTIONf_plane_restr0.005388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.150.32391070.23321965X-RAY DIFFRACTION80
2.15-2.260.23831320.19012368X-RAY DIFFRACTION97
2.26-2.410.18781170.16152486X-RAY DIFFRACTION100
2.41-2.590.18391470.14962439X-RAY DIFFRACTION100
2.59-2.850.20551530.15672476X-RAY DIFFRACTION100
2.85-3.270.1821690.14652462X-RAY DIFFRACTION100
3.27-4.110.16961250.13412501X-RAY DIFFRACTION100
4.11-39.520.16811300.15942644X-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)
10.76910.3269-0.89762.047-0.87191.4937-0.01620.03470.0832-0.0208-0.04550.1722-0.02580.04710.03410.144-0.00220.01040.12730.00270.1795-24.518720.766121.2068
20.8849-0.10060.1580.4688-0.13950.6871-0.0348-0.02580.01530.00950.04980.02160.0207-0.0096-0.01770.16380.00350.00520.1394-0.00140.154-21.027221.326921.632
33.17791.7637-0.27982.8575-0.22921.1637-0.03310.0066-0.3751-0.0168-0.026-0.34290.16850.21970.04610.18560.03160.00650.1745-0.03960.166-6.996314.851615.3714
40.89410.3379-0.13271.8798-0.55020.709-0.11080.1522-0.0120.0180.0931-0.1452-0.00360.08780.020.1842-0.012-0.00820.16310.030.1659-13.848529.807112.1467
51.78241.46990.34744.6150.10980.8711-0.16890.2680.0267-0.37190.1155-0.1416-0.0190.20770.03260.1946-0.00280.02320.2680.00040.1901-6.932924.62257.0235
60.7649-0.36270.07760.9504-0.6120.8693-0.01540.12540.1187-0.04260.00660.1152-0.076-0.01890.01320.1855-0.0228-0.00050.18840.01540.1896-23.332232.85219.0955
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 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 293 )

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