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- PDB-9l3b: Crystal structure of AnAChE N267D-Y269W mutant -

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Basic information

Entry
Database: PDB / ID: 9l3b
TitleCrystal structure of AnAChE N267D-Y269W 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: 1.76 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 18, 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
Water5,855325
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)79.123, 79.123, 92.084
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-355-

HOH

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Components

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


Mass: 32400.859 Da / Num. of mol.: 1 / Mutation: N267D,Y269W
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.: 325 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
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: 1.76→54.97 Å / Num. obs: 33489 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Net I/σ(I): 20.5
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 18 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1886 / CC1/2: 0.955 / % possible all: 99.8

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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: 1.76→54.97 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1641 1696 5.07 %
Rwork0.137 --
obs0.1383 33450 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→54.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 0 325 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112216
X-RAY DIFFRACTIONf_angle_d1.0543038
X-RAY DIFFRACTIONf_dihedral_angle_d5.62305
X-RAY DIFFRACTIONf_chiral_restr0.067322
X-RAY DIFFRACTIONf_plane_restr0.009399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.810.19641500.15722568X-RAY DIFFRACTION100
1.81-1.870.18541290.13772649X-RAY DIFFRACTION100
1.87-1.940.18591340.14842612X-RAY DIFFRACTION100
1.94-2.020.20551630.13722597X-RAY DIFFRACTION100
2.02-2.110.1751490.132580X-RAY DIFFRACTION100
2.11-2.220.15541310.12362638X-RAY DIFFRACTION100
2.22-2.360.16871280.14042658X-RAY DIFFRACTION100
2.36-2.540.161250.13272666X-RAY DIFFRACTION100
2.54-2.80.17281580.1442623X-RAY DIFFRACTION100
2.8-3.20.15231510.13422652X-RAY DIFFRACTION100
3.2-4.030.13981440.12422698X-RAY DIFFRACTION100
4.03-54.970.16541340.14822813X-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)
12.5677-0.25-0.26671.38781.12212.10040.0126-0.00470.09920.02-0.01040.065-0.1067-0.12770.02680.12410.00510.01090.11810.00530.125730.310710.84976.1177
20.56880.0662-0.09690.67090.05210.7230.027-0.00940.0383-0.0299-0.01790.0102-0.0525-0.058-0.01080.15180.01140.00040.1481-0.00140.145528.83197.52156.5935
31.3028-1.3063-0.20356.67061.02761.02650.01550.0629-0.0883-0.077-0.08450.34330.03-0.22810.11710.1457-0.014-0.02550.22320.00170.173416.3003-1.24790.1867
43.1263-2.4304-0.68553.32570.69860.9613-0.1234-0.1218-0.1093-0.01880.09980.06710.0413-0.06320.05060.1646-0.00190.02080.1395-0.00370.144432.8494-2.8124-3.0946
54.881-4.28090.37756.6249-0.27421.14450.10630.2071-0.134-0.4017-0.13760.13210.0864-0.11570.02090.1898-0.0302-0.00080.1673-0.01650.125424.5881-6.0911-8.5185
62.9192-1.6982-0.37611.9834-0.01270.49950.02270.1591-0.0181-0.2094-0.0296-0.038-0.0743-0.0884-0.01560.217-0.0085-0.00150.1772-0.01040.137232.25153.0169-10.2949
71.5794-0.1734-0.62160.96550.37931.4863-0.04810.00210.0014-0.07730.0386-0.14420.01390.1210.0060.1715-0.00680.02640.1479-0.00570.171243.2184.1768-4.434
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 243 )
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 293 )

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