[English] 日本語
Yorodumi
- PDB-1ax9: ACETYLCHOLINESTERASE COMPLEXED WITH EDROPHONIUM, LAUE DATA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ax9
TitleACETYLCHOLINESTERASE COMPLEXED WITH EDROPHONIUM, LAUE DATA
ComponentsACETYLCHOLINESTERASE
KeywordsHYDROLASE / CARBOXYLIC ESTERASE / SERINE ESTERASE / SYNAPSE
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / choline metabolic process / side of membrane / synaptic cleft / synapse / extracellular space / 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, catalytic domain / Alpha/Beta hydrolase fold ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
EDROPHONIUM ION / Acetylcholinesterase
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRaves, M.L. / Ravelli, R.B.G. / Sussman, J.L. / Harel, M. / Silman, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Static Laue diffraction studies on acetylcholinesterase.
Authors: Ravelli, R.B. / Raves, M.L. / Ren, Z. / Bourgeois, D. / Roth, M. / Kroon, J. / Silman, I. / Sussman, J.L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Quaternary Ligand Binding to Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase
Authors: Harel, M. / Schalk, I. / Ehret-Sabatier, L. / Bouet, F. / Goeldner, M. / Hirth, C. / Axelsen, P.H. / Silman, I. / 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.
#3: Journal: J.Mol.Biol. / Year: 1988
Title: Purification and Crystallization of a Dimeric Form of Acetylcholinesterase from Torpedo Californica Subsequent to Solubilization with Phosphatidylinositol-Specific Phospholipase C
Authors: Sussman, J.L. / Harel, M. / Frolow, F. / Varon, L. / Toker, L. / Futerman, A.H. / Silman, I.
History
DepositionNov 3, 1997Processing site: BNL
Revision 1.0Feb 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 2, 2021Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_biol / struct_site
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Category: 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)60,9032
Polymers60,7371
Non-polymers1661
Water2,594144
1
A: ACETYLCHOLINESTERASE
hetero molecules

A: ACETYLCHOLINESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,8064
Polymers121,4732
Non-polymers3322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2830 Å2
ΔGint-5 kcal/mol
Surface area35850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.000, 113.000, 136.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein ACETYLCHOLINESTERASE


Mass: 60736.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Torpedo californica (Pacific electric ray)
Organ: ELECTRIC ORGAN / References: UniProt: P04058, acetylcholinesterase
#2: Chemical ChemComp-EDR / EDROPHONIUM ION


Mass: 166.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16NO / Comment: neurotransmitter, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 277 K / pH: 5.8
Details: PROTEIN WAS CRYSTALLISED FROM 40 % PEG200, 100 MM MES, PH 5.8 AT 4 DEGREES C, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Raves, M.L., (1997) Nature Struct.Biol., 4, 57.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
138 %PEG2001reservoir
20.1 MMES1reservoir
312 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.4
DetectorDetector: CCD / Date: Apr 30, 1995
RadiationMonochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 0.4 Å / Relative weight: 1
ReflectionResolution: 2.8→20.2 Å / Num. obs: 21492 / % possible obs: 84.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.148
Reflection shellResolution: 2.8→3 Å / Rsym value: 0.25 / % possible all: 61.3
Reflection
*PLUS
Num. measured all: 83171 / Rmerge(I) obs: 0.148

-
Processing

Software
NameClassification
LaueViewdata collection
LaueViewdata reduction
REFMACrefinement
LaueViewdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACE

2ace


Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1032 4.8 %RANDOM
obs0.207 21490 84.5 %-
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 12 144 4308

+
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://pdbjlvh1.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