[English] 日本語
Yorodumi
- PDB-7wao: Glutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wao
TitleGlutamyl-tRNA synthetase from Plasmodium falciparum (PfERS) in complex with Mn
ComponentsGlutamyl-tRNA synthetase
KeywordsLIGASE / ERS / GluRS / GLUTAMYL-TRNA SYNTHETASE / AMINOACYL-TRNA SYNTHETAS / AMINOACYLATION / Manganese
Function / homology
Function and homology information


methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / ATP binding / metal ion binding / cytosol
Similarity search - Function
Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain ...Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
Similarity search - Domain/homology
: / glutamate--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.582 Å
AuthorsSharma, V. / Manickam, Y. / Babbar, P. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
CitationJournal: Mol.Biochem.Parasitol. / Year: 2022
Title: Structural characterization of glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum.
Authors: Sharma, V.K. / Chhibber-Goel, J. / Yogavel, M. / Sharma, A.
History
DepositionDec 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: Glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,75810
Polymers61,3611
Non-polymers3979
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-49 kcal/mol
Surface area22940 Å2
Unit cell
Length a, b, c (Å)156.750, 46.880, 94.530
Angle α, β, γ (deg.)90.000, 108.880, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Glutamyl-tRNA synthetase


Mass: 61361.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1349200 / Plasmid: pETM41 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IDK7, glutamate-tRNA ligase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30 % w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.58→45.33 Å / Num. obs: 20654 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 1 / Rrim(I) all: 0.123 / Net I/σ(I): 11.1
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1370 / CC1/2: 0.69 / Rrim(I) all: 1.224 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
PHENIX1.15rc1_3423refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NYL

1nyl


Resolution: 2.582→45.329 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 1033 5 %
Rwork0.1856 19612 -
obs0.1886 20645 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.1 Å2 / Biso mean: 72.6913 Å2 / Biso min: 28.91 Å2
Refinement stepCycle: final / Resolution: 2.582→45.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 9 10 3962
Biso mean--106.26 58.65 -
Num. residues----502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.582-2.71810.321400.2658264994
2.7181-2.88840.40821450.27932772100
2.8884-3.11140.33211480.24622813100
3.1114-3.42440.30111480.22172803100
3.4244-3.91960.28511490.18672832100
3.9196-4.93740.18871490.14442826100
4.9374-45.3290.2011540.16652917100
Refinement TLS params.Method: refined / Origin x: -26.0765 Å / Origin y: -10.1249 Å / Origin z: 19.5027 Å
111213212223313233
T0.3392 Å20.003 Å2-0.019 Å2-0.3723 Å2-0.0181 Å2--0.4353 Å2
L0.2733 °20.171 °2-0.0042 °2-1.0593 °21.2191 °2--2.9397 °2
S0.0032 Å °-0.1375 Å °0.0175 Å °-0.0559 Å °0.0882 Å °-0.0301 Å °-0.2223 Å °0.2635 Å °-0.0682 Å °
Refinement TLS groupSelection details: all

+
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