[English] 日本語
Yorodumi
- PDB-8d8y: Crystal structure of ChoE N147A mutant in complex with acetylthio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d8y
TitleCrystal structure of ChoE N147A mutant in complex with acetylthiocholine
ComponentsChoE
KeywordsHYDROLASE / esterase
Function / homology
Function and homology information


cholinesterase activity / extracellular region
Similarity search - Function
: / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase / SGNH hydrolase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYLTHIOCHOLINE / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL / ChoE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsPham, V.D. / Shi, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT)183530 Canada
CitationJournal: To be published
Title: Crystal structures of bacterial acetylcholinesterase ChoE provide insights into the plasticity of catalytic Ser in regulating the active site geometry and the functional state of the SGNH hydrolases
Authors: Pham, V.D. / Couture, M. / Lortie, L.-A. / Picard, M.-E. / Charette, S. / Levesque, R. / Shi, R.
History
DepositionJun 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ChoE
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,82110
Polymers63,0012
Non-polymers8208
Water10,665592
1
A: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9105
Polymers31,5001
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9105
Polymers31,5001
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.632, 81.786, 81.258
Angle α, β, γ (deg.)90.000, 99.830, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein ChoE


Mass: 31500.266 Da / Num. of mol.: 2 / Mutation: N147A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: choE, PA4921 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HUP2

-
Non-polymers , 5 types, 600 molecules

#2: Chemical ChemComp-AT3 / ACETYLTHIOCHOLINE / 2-{[(1S)-1-HYDROXYETHYL]THIO}-N,N,N-TRIMETHYLETHANAMINIUM


Mass: 162.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ETM / 2-(TRIMETHYLAMMONIUM)ETHYL THIOL


Mass: 120.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14NS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 % / Mosaicity: 0.11 °
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5 / Details: 25% PEG 8000, 0.1M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.54→80.064 Å / Num. all: 83290 / Num. obs: 83290 / % possible obs: 96 % / Redundancy: 3.4 % / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Rsym value: 0.045 / Net I/av σ(I): 10.4 / Net I/σ(I): 14.5 / Num. measured all: 281950
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.54-1.6230.4921.630791103290.3410.6020.4922.481.8
1.62-1.723.50.3362.241425118780.2140.40.3363.899.3
1.72-1.843.40.2073.537364110130.1330.2470.2075.798.1
1.84-1.993.50.1245.936205103610.0780.1470.1249.198.6
1.99-2.183.40.0739.73274195170.0470.0880.07314.398.8
2.18-2.433.40.053132911784860.0340.0630.05319.597.6
2.43-2.813.40.04116.12627176200.0260.0480.04124.398.6
2.81-3.443.40.032192196663770.020.0380.03231.597.9
3.44-4.873.40.02821.51669049480.0180.0330.02838.297.6
4.87-44.9623.40.02620.7938027610.0160.0310.02637.897.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UQV

6uqv


Resolution: 1.54→45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1509 / FOM work R set: 0.8568 / SU B: 1.563 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0725 / SU Rfree: 0.0753 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 4076 4.9 %RANDOM
Rwork0.1536 ---
obs0.1551 79187 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91 Å2 / Biso mean: 22.315 Å2 / Biso min: 9.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å2-0 Å20.13 Å2
2---1 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.54→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 0 48 592 5092
Biso mean--41.59 35.42 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134700
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174278
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.6456412
X-RAY DIFFRACTIONr_angle_other_deg1.5321.589853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.47520.314287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46215701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4581551
X-RAY DIFFRACTIONr_chiral_restr0.0930.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021112
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 245 -
Rwork0.269 4523 -
all-4768 -
obs--74.53 %

+
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