[English] 日本語
Yorodumi
- PDB-8pos: Crystal structure of wolbachia leucyl-tRNA synthetase editing dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pos
TitleCrystal structure of wolbachia leucyl-tRNA synthetase editing domain bound to cmpd9-AMP adduct
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: 2.137 Å
AuthorsPalencia, A. / Hoffmann, G.
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6476
Polymers39,9602
Non-polymers1,6874
Water1,67593
1
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8233
Polymers19,9801
Non-polymers8432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8233
Polymers19,9801
Non-polymers8432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.147, 52.147, 273.558
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 19980.117 Da / Num. of mol.: 2 / 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 / Details (production host): pET-M11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q5GS31, leucine-tRNA ligase
#2: Chemical ChemComp-7RZ / [(1R,3'S,5S,6R,8R)-3'-(aminomethyl)-8-(6-aminopurin-9-yl)-4'-bromanyl-7'-[3-[methyl-(phenylmethyl)amino]propoxy]spiro[2,4,7-trioxa-3$l^{4}-borabicyclo[3.3.0]octane-3,1'-3H-2,1$l^{4}-benzoxaborole]-6-yl]methyl dihydrogen phosphate / AMP adduct with 3-[[(3S)-3-(aminomethyl)-4-bromanyl-1,3-dihydro-2,1-benzoxaborol-7-yl]oxy]-N-methyl-N-(phenylmethyl)propan-1-amine


Type: RNA OH 3 prime terminus / Mass: 747.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H35BBrN7O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 0.2 M LiSO4 ; 31% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.137→51.224 Å / Num. obs: 15552 / % possible obs: 93 % / Redundancy: 29.5 % / CC1/2: 0.999 / Rpim(I) all: 0.04 / Net I/σ(I): 12.1
Reflection shellResolution: 2.137→2.386 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 777 / CC1/2: 0.776 / Rpim(I) all: 0.478

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.137→19.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.413 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.469 / SU Rfree Blow DPI: 0.263 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 780 -RANDOM
Rwork0.2117 ---
obs0.2137 15508 70.2 %-
Displacement parametersBiso mean: 55.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.5543 Å20 Å20 Å2
2--1.5543 Å20 Å2
3----3.1086 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.137→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 106 93 2798
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072781HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.913775HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d976SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes479HARMONIC5
X-RAY DIFFRACTIONt_it2781HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion371SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1823SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion14.85
LS refinement shellResolution: 2.14→2.31 Å
RfactorNum. reflection% reflection
Rfree0.387 22 -
Rwork0.3028 --
obs0.3068 398 8.76 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7735-1.52290.963.9719-1.46972.21380.3636-0.73920.5097-0.7392-0.2940.37250.50970.3725-0.06950.09350.07080.01460.105-0.0075-0.142213.3895-19.607711.0908
21.39070.18950.80011.07790.87764.71410.25050.08040.59330.08040.1139-0.0680.5933-0.068-0.36440.01050.0162-0.0426-0.04030.0873-0.03319.9661-25.554442.243
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A221 - 418
2X-RAY DIFFRACTION1{ A|* }A501
3X-RAY DIFFRACTION2{ B|* }B222 - 418
4X-RAY DIFFRACTION2{ B|* }B501 - 2

+
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