[English] 日本語
Yorodumi
- PDB-9l2p: Crystal structure of AnAChE S34A mutant in complex with propionic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9l2p
TitleCrystal structure of AnAChE S34A mutant in complex with propionic acid
ComponentsCellulose-binding GDSL lipase/acylhydrolase
KeywordsHYDROLASE / Acetylcholinesterase / SGNH hydrolase / GDSL family / S34A
Function / homology: / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / PROPANOIC ACID / Cellulose-binding GDSL lipase/acylhydrolase
Function and homology information
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,4352
Polymers32,3611
Non-polymers741
Water6,179343
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)78.598, 78.598, 91.390
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-412-

HOH

-
Components

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


Mass: 32360.836 Da / Num. of mol.: 1 / Mutation: S34A
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-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
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

-
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: 1.6→39.3 Å / Num. obs: 43344 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 14.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 28.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 16.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 2123 / CC1/2: 0.971 / % possible all: 99.7

-
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: 1.6→37.94 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1568 2154 4.97 %
Rwork0.1371 --
obs0.1381 43307 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→37.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 5 343 2454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162208
X-RAY DIFFRACTIONf_angle_d1.53025
X-RAY DIFFRACTIONf_dihedral_angle_d5.943307
X-RAY DIFFRACTIONf_chiral_restr0.092322
X-RAY DIFFRACTIONf_plane_restr0.012397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.18551620.15092670X-RAY DIFFRACTION100
1.64-1.680.14511220.1272736X-RAY DIFFRACTION100
1.68-1.730.14261450.12422704X-RAY DIFFRACTION100
1.73-1.780.14581570.12022688X-RAY DIFFRACTION100
1.78-1.840.14431640.12332699X-RAY DIFFRACTION100
1.84-1.90.17511200.12752733X-RAY DIFFRACTION100
1.9-1.980.16961510.1272749X-RAY DIFFRACTION100
1.98-2.070.15831400.12342708X-RAY DIFFRACTION100
2.07-2.180.18261420.12852714X-RAY DIFFRACTION100
2.18-2.310.15721320.13292769X-RAY DIFFRACTION100
2.31-2.490.14191390.13682720X-RAY DIFFRACTION100
2.49-2.740.15471280.14582795X-RAY DIFFRACTION100
2.74-3.140.19121290.14042781X-RAY DIFFRACTION100
3.14-3.950.15251760.13372771X-RAY DIFFRACTION100
3.95-37.940.13811470.15622916X-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)
12.2275-0.65120.31981.347-1.15571.96010.0232-0.0017-0.08940.0077-0.0438-0.01470.0418-0.04780.03220.0912-0.0069-0.01240.10350.00370.1128-30.1055-10.876.0664
20.40450.14630.17640.5930.13050.49960.0568-0.0262-0.06210.0207-0.02430.00730.0437-0.0715-0.01020.1110.006-0.00640.13360.00980.1197-33.3715-9.48247.1295
30.677-0.18130.15762.37120.27020.97330.0334-0.1078-0.08720.0293-0.0461-0.08530.09850.0565-0.03760.10830.00170.00070.14170.01470.1185-20.1166-10.627311.6659
40.6263-0.11370.19961.8343-0.17840.9173-0.0017-0.00250.0235-0.1056-0.0039-0.0392-0.06070.01920.00440.09930.0069-0.00220.1073-0.00290.0979-25.2203-1.26031.2088
51.191-0.83360.25073.842-0.22750.76490.01170.04220.0833-0.0587-0.0415-0.18-0.11310.12470.04190.1308-0.00630.02310.14460.00420.126-16.28281.25070.2437
61.8242-0.97780.64971.6182-0.34280.7626-0.00550.01750.0892-0.1155-0.05670.0271-0.099-0.03410.02330.11690.0119-0.0150.10820.0090.0986-32.55572.8344-3.0676
73.7978-3.5908-0.38135.40860.48240.79690.0560.16690.0572-0.2776-0.1036-0.0362-0.07140.04810.03020.1851-0.0138-0.00530.13840.01810.1128-24.74126.1949-8.1978
82.0048-0.97470.42471.3725-0.03720.7320.03020.0629-0.0307-0.2004-0.03120.0324-0.00230.01550.01970.16690.0034-0.00750.13190.00980.1034-32.0274-2.9807-10.2429
90.80620.12710.48960.84310.10161.1233-0.0498-0.04140.0252-0.060.0280.1857-0.1144-0.22620.05450.14950.0406-0.02880.194-0.00660.1857-48.01751.7119-2.5478
102.5969-1.15980.27511.8159-0.04241.11970.1030.1809-0.099-0.2433-0.07030.0080.0754-0.0316-0.02750.15460.0003-0.01920.145-0.00580.1299-36.2014-11.4768-7.066
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 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 172 )
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 195 )
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 224 )
8X-RAY DIFFRACTION8chain 'A' and (resid 225 through 243 )
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 272 )
10X-RAY DIFFRACTION10chain 'A' and (resid 273 through 293 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more