[English] 日本語
Yorodumi
- PDB-4p2b: Crystal structure of the apo form of the glutaminyl-tRNA syntheta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p2b
TitleCrystal structure of the apo form of the glutaminyl-tRNA synthetase catalytic domain from Toxoplasma gondii.
ComponentsGlutamine aminoacyl-tRNA synthetase
KeywordsLIGASE / aminoacyl tRNA synthetase
Function / homology
Function and homology information


glutamine-tRNA ligase / glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Glutamine-tRNA synthetase / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Ribosomal Protein L25; Chain P / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Ribosomal Protein L25; Chain P ...Glutamine-tRNA synthetase / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA Synthetase; domain 2 / Glutamyl-trna Synthetase; Domain 2 / Glutamyl-tRNA Synthetase; domain 3 / Glutamyl-tRNA Synthetase; Domain 3 / Ribosomal Protein L25; Chain P / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Ribosomal Protein L25; Chain P / 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. / HUPs / 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 / Alpha-Beta Complex / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamine--tRNA ligase / Glutamine--tRNA ligase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Authorsvan Rooyen, J.M. / Belrhali, H. / Hakimi, M.A.
Funding support France, India, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV3-0009-01 France
Laboratoire d'Excellence ParaFrapANR-11-LABX-0024 France
Fondation Innovations en Infectiologie France
Outstanding Scientist Research Programme of the Department of Biotechnology India
CitationJournal: To Be Published
Title: Crystal structure of the apo form of the glutaminyl-tRNA synthetase catalytic domain from Toxoplasma gondii.
Authors: van Rooyen, J.M. / Belrhali, H. / Hakimi, M.A.
History
DepositionMar 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Experimental preparation
Revision 1.2Oct 4, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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: Glutamine aminoacyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6053
Polymers66,4131
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-19 kcal/mol
Surface area23410 Å2
MethodPISA
2
A: Glutamine aminoacyl-tRNA synthetase
hetero molecules

A: Glutamine aminoacyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2116
Polymers132,8262
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area2920 Å2
ΔGint-63 kcal/mol
Surface area44480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.130, 105.130, 229.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Glutamine aminoacyl-tRNA synthetase


Mass: 66413.156 Da / Num. of mol.: 1 / Fragment: UNP residues 332-886
Source method: isolated from a genetically manipulated source
Details: Database gene sequence was optimized for codon usage before synthesis.
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D3XAP9, UniProt: B6KTZ0*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 5.54 Å3/Da / Density % sol: 77.82 % / Description: Amygdaloidal
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1 ul 40 g/L protein to 1 ul 2M ammonium sulphate over 2M ammonium sulphate reservoir.
PH range: unbuffered

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→35.6 Å / Num. obs: 36436 / % possible obs: 98.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.4
Reflection shellResolution: 2.8→2.92 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 1.3 / % possible all: 98.4

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qtq

1qtq


Resolution: 2.8→35.6 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1824 5.02 %random selection
Rwork0.225 ---
obs0.2266 36328 98.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 10 0 3840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093928
X-RAY DIFFRACTIONf_angle_d1.3685347
X-RAY DIFFRACTIONf_dihedral_angle_d16.9261350
X-RAY DIFFRACTIONf_chiral_restr0.095598
X-RAY DIFFRACTIONf_plane_restr0.007694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87570.45871390.41932580X-RAY DIFFRACTION98
2.8757-2.96030.37021330.35322645X-RAY DIFFRACTION99
2.9603-3.05580.3731340.2842641X-RAY DIFFRACTION99
3.0558-3.16490.32851360.27262623X-RAY DIFFRACTION99
3.1649-3.29150.32431290.2712654X-RAY DIFFRACTION99
3.2915-3.44120.3141310.26652629X-RAY DIFFRACTION99
3.4412-3.62250.26371610.2282633X-RAY DIFFRACTION99
3.6225-3.84920.27161320.21392629X-RAY DIFFRACTION98
3.8492-4.1460.25031380.1892665X-RAY DIFFRACTION98
4.146-4.56250.20161560.16482664X-RAY DIFFRACTION98
4.5625-5.22090.18821520.17152651X-RAY DIFFRACTION98
5.2209-6.5710.26381460.23392705X-RAY DIFFRACTION98
6.571-35.6660.24761370.24352785X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / 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)
11.2817-1.1464-0.54182.5798-0.85191.7816-0.1952-0.05960.1710.21210.0441-0.0208-0.26330.08630.04590.69250.0397-0.07370.3442-0.0190.504576.680273.700757.4247
22.7259-0.9289-1.00240.65250.90811.3692-0.2322-0.00190.18850.22840.0490.0250.21560.2380.15070.67670.0290.0380.29680.06850.523599.498647.632750.8232
31.6947-0.9571-1.3842.14910.00691.4907-0.1683-0.107-0.26150.598-0.00050.2340.0058-0.0060.14790.80710.04980.10030.3461-0.06230.4431117.099424.906344.5062
41.11431.3739-0.62161.7174-0.38626.0348-0.2435-0.2271-0.2897-0.02130.123-0.12680.53190.0497-0.02490.63910.19960.28260.50650.33910.340572.434748.838679.7033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 40:271
2X-RAY DIFFRACTION2chain A and resid 272:359
3X-RAY DIFFRACTION3chain A and (resid 360 through 479 )
4X-RAY DIFFRACTION4chain A and resid 18:36

+
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://pdbjlc1.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