3W1J Transferase date Nov 15, 2012
title Crystal Structure Of The N-Terminal Truncated Selenocysteine Sela In Complex With Thiosulfate
authors Y.Itoh, S.Sekine, S.Yokoyama
compound source
Molecule: L-Seryl-Trna(Sec) Selenium Transferase
Chain: A, B, C, D, E, F, G, H, I, J
Fragment: The Core And C-Terminal Domains, Unp Residues 62-
Synonym: Selenocysteine Synthase, Sec Synthase, Selenocyste Trna(Sec) Synthase;
Ec: 2.9.1.1
Engineered: Yes
Organism_scientific: Aquifex Aeolicus
Organism_taxid: 224324
Strain: Vf5
Gene: Sela
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 1
R_factor 0.200 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.442 116.372 124.788 102.09 93.39 106.06
method X-Ray Diffractionresolution 3.25 Å
ligand K, LLP, THJ enzyme Transferase E.C.2.9.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, E, B, H, C, D, I, G


Primary referenceDecameric SelA*tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation., Itoh Y, Brocker MJ, Sekine S, Hammond G, Suetsugu S, Soll D, Yokoyama S, Science. 2013 Apr 5;340(6128):75-8. doi: 10.1126/science.1229521. PMID:23559248
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1349 Kb) [Save to disk]
  • Biological Unit Coordinates (3w1j.pdb1.gz) 1336 Kb
  • LPC: Ligand-Protein Contacts for 3W1J
  • CSU: Contacts of Structural Units for 3W1J
  • Structure Factors (587 Kb)
  • Retrieve 3W1J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3W1J from S2C, [Save to disk]
  • Re-refined 3w1j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3W1J 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 3W1J
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3W1J, from MSDmotif at EBI
  • Fold representative 3w1j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3w1j_J] [3w1j_I] [3w1j_E] [3w1j_H] [3w1j] [3w1j_A] [3w1j_C] [3w1j_G] [3w1j_D] [3w1j_F] [3w1j_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3W1J
  • Community annotation for 3W1J at PDBWiki (http://pdbwiki.org)

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