[English] 日本語
- PDB-4rri: K116M mutant of N-terminal editing domain of threonyl-tRNA synthe... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 4rri
TitleK116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA
ComponentsProbable threonine--tRNA ligase 2
KeywordsLIGASE / DTD-like fold / Proofreading
Function / homology
Function and homology information

threonine-tRNA ligase activity / threonyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Threonyl-tRNA synthetase, editing domain, archaea / D-aminoacyl-tRNA deacylase-like superfamily / Archaea-specific editing domain of threonyl-tRNA synthetase / Anticodon-binding domain superfamily / Threonine-tRNA ligase, class IIa / Anticodon-binding / D-tyrosyl-tRNA(Tyr) deacylase / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / 3-Layer(bba) Sandwich / Alpha Beta
Threonine--tRNA ligase editing subunit
Biological speciesAeropyrum pernix (archaea)
AuthorsAhmad, S. / Muthukumar, S. / Sankaranarayanan, R.
CitationJournal: Nat Commun / Year: 2015
Title: Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Authors: Ahmad, S. / Muthukumar, S. / Kuncha, S.K. / Routh, S.B. / Yerabham, A.S. / Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Sankaranarayanan, R.
Validation Report
SummaryFull reportAbout validation report
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: Probable threonine--tRNA ligase 2
hetero molecules

Theoretical massNumber of molelcules
Total (without water)15,5293
A: Probable threonine--tRNA ligase 2
hetero molecules

A: Probable threonine--tRNA ligase 2
hetero molecules

Theoretical massNumber of molelcules
Total (without water)31,0586
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2090 Å2
ΔGint-5 kcal/mol
Surface area11960 Å2
Unit cell
Length a, b, c (Å)47.119, 47.119, 113.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions





#1: Protein Probable threonine--tRNA ligase 2 / Threonyl-tRNA synthetase 2 / ThrRS 2

Mass: 15137.429 Da / Num. of mol.: 1 / Fragment: UNP residues 1-136 / Mutation: K116M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: thrS2, APE_0117.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YFY3, threonine-tRNA ligase
#2: Chemical ChemComp-A3T / 3'-deoxy-3'-(L-threonylamino)adenosine

Mass: 367.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N7O5
#3: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium

Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl pH 8.5, 0.2M MgCl2, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2012
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 20109 / Num. obs: 19968 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2


CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.65 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1083 5.1 %RANDOM
Rwork0.191 ---
Obs0.195 19968 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 27 100 1194
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021123
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9971529
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00121.59144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20815173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.671158
X-RAY DIFFRACTIONr_chiral_restr0.120.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022853
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.08831123
X-RAY DIFFRACTIONr_sphericity_free30.342534
X-RAY DIFFRACTIONr_sphericity_bonded16.28351157
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.515 70 -
Rwork0.402 1237 -
Obs--96.17 %

About Yorodumi


Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more


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.

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