3KFU Ligase Rna date Oct 28, 2009
title Crystal Structure Of The Transamidosome
authors M.Blaise, M.Bailly, M.Frechin, S.Thirup, H.D.Becker, D.Kern
compound source
Molecule: Non-Discriminating And Archaeal-Type Aspartyl-Trn Synthetase;
Chain: A, B, C, D
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Gene: Ttha1452
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Glutamyl-Trna(Gln) Amidotransferase Subunit A
Chain: E, H
Synonym: Glu-Adt Subunit A
Ec: 6.3.5.-
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Gata, Ttha0573
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Aspartylglutamyl-Trna(Asngln) Amidotransferase
Chain: F, I
Synonym: Aspglu-Adt Subunit B
Ec: 6.3.5.-
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Gatb, Ttha0366
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Glutamyl-Trna(Gln) Amidotransferase Subunit C
Chain: G, J
Synonym: Glu-Adt Subunit C
Ec: 6.3.5.-
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Gatc, Ttha0876
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Trna-Asn
Chain: K, L, M, N
Engineered: Yes

Organism_scientific: Thermus Thermophilus
Organism_taxid: 300852
Strain: Hb8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.199 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
115.920 214.000 127.840 90.00 93.36 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand 5MU, H2U, MG, PSU, ZN enzyme Ligase E.C.6.3.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B, C, D


E, H


F, I


J, G


Primary referenceCrystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation., Blaise M, Bailly M, Frechin M, Behrens MA, Fischer F, Oliveira CL, Becker HD, Pedersen JS, Thirup S, Kern D, EMBO J. 2010 Sep 15;29(18):3118-29. Epub 2010 Aug 17. PMID:20717102
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1391 Kb) [Save to disk]
  • Biological Unit Coordinates (3kfu.pdb1.gz) 1381 Kb
  • LPC: Ligand-Protein Contacts for 3KFU
  • CSU: Contacts of Structural Units for 3KFU
  • Structure Factors (1030 Kb)
  • Retrieve 3KFU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KFU from S2C, [Save to disk]
  • Re-refined 3kfu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KFU in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3KFU
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3KFU, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kfu_J] [3kfu_M] [3kfu_N] [3kfu_D] [3kfu_G] [3kfu_L] [3kfu_C] [3kfu_B] [3kfu_F] [3kfu_E] [3kfu_H] [3kfu] [3kfu_I] [3kfu_K] [3kfu_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3KFU
  • Community annotation for 3KFU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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