[English] 日本語
Yorodumi
- PDB-6wqt: Xanthomonas citri Methionyl-tRNA synthetase in complex with REP3123 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wqt
TitleXanthomonas citri Methionyl-tRNA synthetase in complex with REP3123
ComponentsMethionine--tRNA ligase
KeywordsLIGASE / CRS3123 / Citrus canker / tRNA / aminoacylation
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. ...Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase, beta subunit, C-terminal / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Chem-U81 / Methionine--tRNA ligase
Similarity search - Component
Biological speciesXanthomonas citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMercaldi, G.F. / Benedetti, C.E.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)11/20468-1 Brazil
Sao Paulo Research Foundation (FAPESP)18/08535-4 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)465440/2014-2 Brazil
Sao Paulo Research Foundation (FAPESP)14/50880-0 Brazil
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium.
Authors: Mercaldi, G.F. / Andrade, M.O. / Zanella, J.L. / Cordeiro, A.T. / Benedetti, C.E.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Methionine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6813
Polymers64,1021
Non-polymers5792
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.335, 84.478, 96.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 64102.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas citri (bacteria) / Strain: 306 / Gene: metG, metS, XAC1386 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8PMP0, methionine-tRNA ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-U81 / 5-[(3-{[(4R)-6,8-dibromo-3,4-dihydro-2H-1-benzopyran-4-yl]amino}propyl)amino]thieno[3,2-b]pyridin-7(6H)-one


Mass: 513.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19Br2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG3350, MgCl2 / PH range: 8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.65→42.24 Å / Num. obs: 74214 / % possible obs: 98.3 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 12.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 2.315 / Num. unique obs: 2797 / CC1/2: 0.459 / Rpim(I) all: 1.222 / Rrim(I) all: 2.633 / % possible all: 76

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.26 Å42.24 Å
Translation6.26 Å42.24 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WQ6

6wq6


Resolution: 1.65→42.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.233 / SU ML: 0.12 / SU R Cruickshank DPI: 0.0994 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.098
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 3762 5.1 %RANDOM
Rwork0.2024 ---
obs0.2039 70348 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.39 Å2 / Biso mean: 33.79 Å2 / Biso min: 22.34 Å2
Baniso -1Baniso -2Baniso -3
1-5.11 Å20 Å2-0 Å2
2---3.01 Å20 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 1.65→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4244 0 28 165 4437
Biso mean--46.11 38.64 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134391
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174000
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6425968
X-RAY DIFFRACTIONr_angle_other_deg1.4231.5769242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1621.652230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9515670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7241529
X-RAY DIFFRACTIONr_chiral_restr0.080.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02992
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 225 -
Rwork0.439 4126 -
all-4351 -
obs--78.97 %

+
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