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- PDB-9l34: Crystal structure of AnAChE H270A mutant -

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Basic information

Entry
Database: PDB / ID: 9l34
TitleCrystal structure of AnAChE H270A mutant
ComponentsCellulose-binding GDSL lipase/acylhydrolase
KeywordsHYDROLASE / Acetylcholinesterase / SGNH hydrolase / GDSL family / H270A
Function / homology: / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / 1,4-DIETHYLENE DIOXIDE / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,6894
Polymers32,3101
Non-polymers3793
Water8,305461
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)79.032, 79.032, 91.811
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-679-

HOH

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Components

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


Mass: 32309.770 Da / Num. of mol.: 1 / Mutation: H270A
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 51.99 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M Ammonium sulfate, 10%(v/v) 1,4-dioxane, 0.1 M 2-Morpholinoethanesulphonic acid, pH 6.5

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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: 1.71→45.91 Å / Num. obs: 36592 / % possible obs: 100 % / Redundancy: 19.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 19.4
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 18.4 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 1904 / CC1/2: 0.941 / % possible all: 99.6

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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
Starting model: 9L1R

9l1r


Resolution: 1.71→38.12 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1645 1894 5.18 %
Rwork0.1436 --
obs0.1447 36538 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 23 461 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072220
X-RAY DIFFRACTIONf_angle_d0.9193043
X-RAY DIFFRACTIONf_dihedral_angle_d6.486319
X-RAY DIFFRACTIONf_chiral_restr0.058325
X-RAY DIFFRACTIONf_plane_restr0.007395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.23061500.19092406X-RAY DIFFRACTION100
1.75-1.80.21331000.16772496X-RAY DIFFRACTION100
1.8-1.850.18551260.16222437X-RAY DIFFRACTION100
1.85-1.910.19671320.1522424X-RAY DIFFRACTION100
1.91-1.980.19061510.16012445X-RAY DIFFRACTION100
1.98-2.060.18161320.14112452X-RAY DIFFRACTION100
2.06-2.150.17191690.14152421X-RAY DIFFRACTION100
2.15-2.260.16371190.1372477X-RAY DIFFRACTION100
2.26-2.40.1661510.14372469X-RAY DIFFRACTION100
2.41-2.590.1771070.14152476X-RAY DIFFRACTION100
2.59-2.850.15261390.15652498X-RAY DIFFRACTION100
2.85-3.260.17891390.14852502X-RAY DIFFRACTION100
3.26-4.110.13621350.12612516X-RAY DIFFRACTION100
4.11-38.120.14751440.13742625X-RAY DIFFRACTION99
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)
11.98530.7479-1.37941.5790.51452.0318-0.01130.08080.04390.00340.00830.1386-0.0843-0.06410.0190.14880.00850.00860.14020.01650.16825.898231.5677-9.1476
21.1761-0.2906-0.35990.55220.04120.97720.05540.01550.07910.04510.02840.0725-0.1219-0.0877-0.07340.1501-0.00760.01530.12460.00480.13288.606833.7425-8.1286
39.1878-1.9919-0.86412.25810.40942.5668-0.0434-0.1619-0.20520.2334-0.03760.19850.0779-0.19890.0820.1851-0.03030.00720.1687-0.00950.1550.725722.8936-3.5968
41.7975-0.3229-0.19381.018-0.1091.07070.05470.0989-0.123-0.0436-0.0670.03050.0862-0.04630.01730.1328-0.0068-0.00330.1287-0.01490.107313.231420.7882-15.8667
56.54660.7280.44511.50520.13381.3111-0.00890.2869-0.1722-0.2054-0.0611-0.02510.1183-0.03280.06630.19920.02380.01580.1583-0.0270.130617.857518.3691-23.6905
62.9940.8197-0.00841.3433-0.19180.98660.05620.28150.0584-0.1413-0.0323-0.0078-0.0081-0.07230.00020.1710.01880.00750.17720.00340.114213.572429.3439-25.63
71.74960.103-0.88841.4129-0.49791.57890.09090.09080.2095-0.0682-0.0455-0.0899-0.22110.1149-0.03160.1750.00620.03620.12590.02260.137118.037339.346-19.8189
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 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 195 )
5X-RAY DIFFRACTION5chain 'A' and (resid 196 through 224 )
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 243 )
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 293 )

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