[English] 日本語
Yorodumi
- PDB-7b38: Torpedo californica acetylcholinesterase complexed with Mg+2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b38
TitleTorpedo californica acetylcholinesterase complexed with Mg+2
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholinesterase / ASSAM / differential scanning calorimetry / divalent metal ion / electron paramagnetic resonance / thermal inactivation / Torpedo / 4D motif / 3.1.1.7
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / side of membrane / synapse / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetylcholinesterase
Similarity search - Component
Biological speciesTetronarce californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSilman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. / Weiner, L.
Citation
Journal: Protein Sci. / Year: 2021
Title: Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif.
Authors: Silman, I. / Shnyrov, V.L. / Ashani, Y. / Roth, E. / Nicolas, A. / Sussman, J.L. / Weiner, L.
#1: Journal: Biochemistry / Year: 2002
Title: X-ray structures of Torpedo californica acetylcholinesterase complexed with (+)-huperzine A and (-)-huperzine B: structural evidence for an active site rearrangement.
Authors: Dvir, H. / Jiang, H.L. / Wong, D.M. / Harel, M. / Chetrit, M. / He, X.C. / Jin, G.Y. / Yu, G.L. / Tang, X.C. / Silman, I. / Bai, D.L. / Sussman, J.L.
#2: Journal: Science / Year: 1991
Title: Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein.
Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Oefner, C. / Goldman, A. / Toker, L. / Silman, I.
History
DepositionNov 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,24022
Polymers60,1941
Non-polymers2,04621
Water7,152397
1
A: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,47944
Polymers120,3882
Non-polymers4,09142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area8290 Å2
ΔGint-51 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.217, 138.217, 71.376
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Acetylcholinesterase / / AChE


Mass: 60193.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Tetronarce californica (Pacific electric ray)
Organ: ELECTRIC ORGAN / Variant: G2 FORM / Tissue: ELECTROPLAQUE / References: UniProt: P04058, acetylcholinesterase

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 7 types, 415 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Mixing 2 uL of protein (10-13 mg/mL in 0.1 M NaCl/0.1 M 2-morpholinoethanesulfonic acid (MES)/0.02% sodium azide, pH 5.8) with 2 uL of precipitant solution (0.2 M magnesium acetate/10-15% ...Details: Mixing 2 uL of protein (10-13 mg/mL in 0.1 M NaCl/0.1 M 2-morpholinoethanesulfonic acid (MES)/0.02% sodium azide, pH 5.8) with 2 uL of precipitant solution (0.2 M magnesium acetate/10-15% (v/v) polyethylene glycol (PEG) 5000 monomethyl ether, 0.1 M MES, pH 6.5), thus yielding crystals of the Mg+2/TcAChE complex
PH range: 5.8

-
Data collection

DiffractionMean temperature: 155 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.85→34.83 Å / Num. obs: 69953 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 28.37 Å2 / CC1/2: 0.85 / Net I/σ(I): 10.6
Reflection shellResolution: 1.86→1.87 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9954 / CC1/2: 0.3 / % possible all: 99.94

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.15.2_3472refinement
DENZOV1.0data reduction
SCALEPACKV1.0data scaling
MERLOTV1.0phasing
Coot9.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EA5

1ea5


Resolution: 1.85→34.83 Å / SU ML: 0.213 / Cross valid method: FREE R-VALUE / Phase error: 26.1539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 3292 4.92 %4.92%
Rwork0.2022 63651 --
obs0.2041 66943 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.12 Å2
Refinement stepCycle: LAST / Resolution: 1.85→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 127 400 4727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714443
X-RAY DIFFRACTIONf_angle_d0.81156016
X-RAY DIFFRACTIONf_chiral_restr0.0519640
X-RAY DIFFRACTIONf_plane_restr0.0051776
X-RAY DIFFRACTIONf_dihedral_angle_d3.53033565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.34431470.29962635X-RAY DIFFRACTION99.04
1.88-1.90.31041150.27822618X-RAY DIFFRACTION99.67
1.9-1.930.3011370.27032659X-RAY DIFFRACTION99.75
1.93-1.960.31891410.26392623X-RAY DIFFRACTION99.89
1.96-20.28161310.25892629X-RAY DIFFRACTION99.75
2-2.040.32331570.26142623X-RAY DIFFRACTION99.96
2.04-2.070.27861230.24642639X-RAY DIFFRACTION99.93
2.07-2.120.26171420.24352635X-RAY DIFFRACTION99.78
2.12-2.160.29821270.23132670X-RAY DIFFRACTION99.86
2.16-2.210.29021290.2472646X-RAY DIFFRACTION99.93
2.21-2.270.25931560.2342591X-RAY DIFFRACTION99.93
2.27-2.330.25871710.22592619X-RAY DIFFRACTION99.71
2.33-2.40.26691480.22232637X-RAY DIFFRACTION99.82
2.4-2.480.27771380.21932644X-RAY DIFFRACTION99.82
2.48-2.560.25841020.22572668X-RAY DIFFRACTION99.82
2.56-2.670.31221340.22272674X-RAY DIFFRACTION99.93
2.67-2.790.24981230.22332670X-RAY DIFFRACTION99.93
2.79-2.930.23371550.21862649X-RAY DIFFRACTION99.89
2.93-3.120.28191560.21472643X-RAY DIFFRACTION99.82
3.12-3.360.23331180.20042694X-RAY DIFFRACTION99.82
3.36-3.70.21551280.18312681X-RAY DIFFRACTION99.68
3.7-4.230.19931290.16672699X-RAY DIFFRACTION99.58
4.23-5.330.19721400.152691X-RAY DIFFRACTION99.47
5.33-34.830.19561450.1792714X-RAY DIFFRACTION96.85

+
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