[English] 日本語
Yorodumi
- PDB-6arx: Crystal structure of an insecticide-resistant acetylcholinesteras... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6arx
TitleCrystal structure of an insecticide-resistant acetylcholinesterase mutant from the malaria vector Anopheles gambiae in the ligand-free state
ComponentsAcetylcholinesterase
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


choline metabolic process / acetylcholine catabolic process / acetylcholinesterase / acetylcholinesterase activity / synapse / extracellular space / plasma membrane
Similarity search - Function
: / 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 ...: / 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
CITRATE ANION / Acetylcholinesterase
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 Å
AuthorsCheung, J. / Mahmood, A. / Kalathur, R. / Lixuan, L. / Carlier, P.R.
CitationJournal: Structure / Year: 2018
Title: Structure of the G119S Mutant Acetylcholinesterase of the Malaria Vector Anopheles gambiae Reveals Basis of Insecticide Resistance.
Authors: Cheung, J. / Mahmood, A. / Kalathur, R. / Liu, L. / Carlier, P.R.
History
DepositionAug 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,69110
Polymers121,2362
Non-polymers1,4558
Water6,485360
1
A: Acetylcholinesterase
hetero molecules

B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,69110
Polymers121,2362
Non-polymers1,4558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area3400 Å2
ΔGint-8 kcal/mol
Surface area41450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.599, 149.599, 225.857
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 163 through 337 or resid 339...
21(chain B and (resid 163 through 337 or resid 339...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEU(chain A and (resid 163 through 337 or resid 339...AA163 - 3373 - 177
12TRPTRPPROPRO(chain A and (resid 163 through 337 or resid 339...AA339 - 351179 - 191
13ARGARGGLNGLN(chain A and (resid 163 through 337 or resid 339...AA353 - 569193 - 409
14TYRTYRALAALA(chain A and (resid 163 through 337 or resid 339...AA571 - 659411 - 499
15GLYGLYASNASN(chain A and (resid 163 through 337 or resid 339...AA661 - 699501 - 539
21ASNASNLEULEU(chain B and (resid 163 through 337 or resid 339...BB163 - 3373 - 177
22TRPTRPPROPRO(chain B and (resid 163 through 337 or resid 339...BB339 - 351179 - 191
23ARGARGGLNGLN(chain B and (resid 163 through 337 or resid 339...BB353 - 569193 - 409
24TYRTYRALAALA(chain B and (resid 163 through 337 or resid 339...BB571 - 659411 - 499
25GLYGLYASNASN(chain B and (resid 163 through 337 or resid 339...BB661 - 699501 - 539

-
Components

#1: Protein Acetylcholinesterase / AChE


Mass: 60617.965 Da / Num. of mol.: 2 / Fragment: residues 162 to 702 / Mutation: G280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: Ace, ACE1, ACHE1, AGAP001356 / Plasmid: modified pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q869C3, acetylcholinesterase
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.02 Å3/Da / Density % sol: 79.56 % / Mosaicity: 0.35 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.9 - 1.0M tri-ammonium citrate pH 6.5, 1 - 3% isopropanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 24, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→200 Å / Num. obs: 125913 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 46.63 Å2
Data reduction details: high redundancy of data and CC1/2 0.3 was used for resolution cut-off
Rmerge(I) obs: 0.21 / Rpim(I) all: 0.077 / Rrim(I) all: 0.224 / Χ2: 1.023 / Net I/σ(I): 3.1 / Num. measured all: 1027353
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.346.52.63462610.3631.092.8590.53399.6
2.34-2.387.92.56663220.4710.9672.7450.534100
2.38-2.438.32.2662280.5650.8292.4090.54100
2.43-2.488.42.08962980.6470.762.2250.548100
2.48-2.538.41.76863280.6550.6421.8830.557100
2.53-2.598.41.5462130.7440.561.640.556100
2.59-2.668.31.30563360.7820.4771.3910.577100
2.66-2.7381.04162850.8460.3891.1120.605100
2.73-2.817.40.82262710.8850.3220.8840.613100
2.81-2.980.69562990.9040.2590.7430.637100
2.9-38.70.55562950.9360.1980.590.663100
3-3.128.70.42163120.9610.1510.4470.759100
3.12-3.268.60.33762950.970.1220.3590.903100
3.26-3.448.40.24562830.9830.090.2611.102100
3.44-3.657.70.18563120.9870.0710.1991.44999.9
3.65-3.938.20.15962970.9890.0590.171.76199.9
3.93-4.338.60.13262880.9920.0480.142.05100
4.33-4.968.30.10963290.9940.040.1172.21100
4.96-6.2480.10263200.9940.0380.1091.85299.8
6.24-2008.40.0763410.9970.0250.0741.82898.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER(1.11.1_2575: ???)phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EY4

4ey4


Resolution: 2.302→49.103 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.21
RfactorNum. reflection% reflectionSelection details
Rfree0.2032 6259 4.98 %RANDOM
Rwork0.1777 ---
obs0.179 125762 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.92 Å2 / Biso mean: 54.2164 Å2 / Biso min: 29.61 Å2
Refinement stepCycle: final / Resolution: 2.302→49.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 95 360 8957
Biso mean--94.53 53.82 -
Num. residues----1074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128935
X-RAY DIFFRACTIONf_angle_d1.16512214
X-RAY DIFFRACTIONf_chiral_restr0.0631297
X-RAY DIFFRACTIONf_plane_restr0.0081616
X-RAY DIFFRACTIONf_dihedral_angle_d11.8795268
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5176X-RAY DIFFRACTION5.377TORSIONAL
12B5176X-RAY DIFFRACTION5.377TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3021-2.32830.37381710.34373785395694
2.3283-2.35570.34092260.318639894215100
2.3557-2.38440.31982000.30539714171100
2.3844-2.41460.32141850.294440144199100
2.4146-2.44630.27791830.296239754158100
2.4463-2.47990.31832240.289439624186100
2.4799-2.51530.32072230.286939954218100
2.5153-2.55280.33142500.272439074157100
2.5528-2.59270.29932160.279239994215100
2.5927-2.63520.28471910.261140094200100
2.6352-2.68070.28381820.25340274209100
2.6807-2.72940.2581960.247239944190100
2.7294-2.78190.26022290.235939454174100
2.7819-2.83870.28491970.234139824179100
2.8387-2.90040.27091730.231540154188100
2.9004-2.96780.26541970.225539884185100
2.9678-3.04210.24082200.211140274247100
3.0421-3.12430.2492270.208139954222100
3.1243-3.21620.24112130.212839404153100
3.2162-3.320.24282430.2139804223100
3.32-3.43860.23021920.190339944186100
3.4386-3.57630.23062460.17239654211100
3.5763-3.7390.16912210.160739914212100
3.739-3.9360.17781860.140840094195100
3.936-4.18250.15422120.12940044216100
4.1825-4.50520.132290.11239894218100
4.5052-4.95820.12432250.10839974222100
4.9582-5.67480.14552230.127939774200100
5.6748-7.14610.16151900.139140434233100
7.1461-49.11460.16341890.14984035422499

+
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