[English] 日本語
Yorodumi
- PDB-8poq: Crystal structure of wolbachia leucyl-tRNA synthetase editing domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8poq
TitleCrystal structure of wolbachia leucyl-tRNA synthetase editing domain
ComponentsLeucine--tRNA ligase
KeywordsLIGASE / Leucine tRNA ligase / ATP binding protein / tRNA aminoacylation for protein translation / cytosolic Reaction catalysed: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Leucine--tRNA ligase
Similarity search - Component
Biological speciesWolbachia endosymbiont strain TRS of Brugia malayi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPalencia, A. / Lukarska, M.
Funding support France, European Union, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-AMRB-0003-01 AntibiOxaborole France
Agence Nationale de la Recherche (ANR)ANR JCJC RC18114CC NovoTargetParasite France
iNEXT653706European Union
CitationJournal: Science Advances / Year: 2024
Title: Targeting A Microbiota Wolbachian Aminoacyl-tRNA Synthetase To Block Its Pathogenic Host
Authors: Palencia, A. / Hoffmann, G. / Lukarska, M. / Clare, R. / Ward, S. / Taylor, M.A. / Ringkjobing Jensen, M.
History
DepositionJul 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine--tRNA ligase
B: Leucine--tRNA ligase
C: Leucine--tRNA ligase
D: Leucine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)79,9204
Polymers79,9204
Non-polymers00
Water19811
1
A: Leucine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)19,9801
Polymers19,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)19,9801
Polymers19,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Leucine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)19,9801
Polymers19,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Leucine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)19,9801
Polymers19,9801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.640, 53.640, 267.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein
Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 19980.117 Da / Num. of mol.: 4 / Mutation: Deletion 354-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont strain TRS of Brugia malayi (bacteria)
Gene: leuS, Wbm0605 / Plasmid: pET-M11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q5GS31, leucine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH8.5; 1 M LiCl2; 18 % w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97549 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97549 Å / Relative weight: 1
ReflectionResolution: 2.85→49.78 Å / Num. obs: 14906 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rrim(I) all: 0.05 / Net I/σ(I): 16.6
Reflection shellResolution: 2.85→3.1 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 739 / CC1/2: 0.72 / Rrim(I) all: 2.19 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.78 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 44.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3263 739 4.96 %
Rwork0.2762 --
obs0.2787 14906 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5103 0 0 11 5114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025198
X-RAY DIFFRACTIONf_angle_d0.5487017
X-RAY DIFFRACTIONf_dihedral_angle_d2.3853125
X-RAY DIFFRACTIONf_chiral_restr0.044815
X-RAY DIFFRACTIONf_plane_restr0.004891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23160.39151600.37492790X-RAY DIFFRACTION99
3.2316-3.55670.36391480.32222839X-RAY DIFFRACTION99
3.5567-4.07120.32311560.28912817X-RAY DIFFRACTION99
4.0712-5.12850.29821460.27352840X-RAY DIFFRACTION100
5.1285-49.780.33271290.26062881X-RAY DIFFRACTION99

+
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