5T8Y Oxidoreductase Rna date Sep 08, 2016
title Structure Of Epoxyqueuosine Reductase From Bacillus Subtilis Asp134 Catalytic Loop Swung Out Of The Active Site.
authors D.P.Dowling, Z.D.Miles, C.Kohrer, S.J.Maiocco, S.J.Elliott, V.Ban C.L.Drennan
compound source
Molecule: Epoxyqueuosine Reductase
Chain: A, B
Synonym: Queuosine Biosynthesis Protein Queg
Ec: 1.17.99.6
Engineered: Yes
Organism_scientific: Bacillus Subtilis (Strain 168)
Organism_taxid: 224308
Strain: 168
Gene: Queg, Ygap, Yhba, Bsu08910
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (5'- R(Gpcpapgpapcpupgpupapapapupcpupgpc)-3');
Chain: X
Engineered: Yes
Other_details: Anticodon Stem Loop Of Tyr-Trna From E. Coli

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.238 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.763 111.030 95.971 90.00 99.13 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand B12, PO4, SF4 enzyme Oxidoreductase E.C.1.17.99.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMolecular basis of cobalamin-dependent RNA modification., Dowling DP, Miles ZD, Kohrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL, Nucleic Acids Res. 2016 Sep 15. pii: gkw806. PMID:27638883
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (5t8y.pdb1.gz) 63 Kb
  • Biological Unit Coordinates (5t8y.pdb2.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 5T8Y
  • CSU: Contacts of Structural Units for 5T8Y
  • Structure Factors (151 Kb)
  • Retrieve 5T8Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5T8Y from S2C, [Save to disk]
  • Re-refined 5t8y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5T8Y 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 5T8Y
  • 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
  • Fold representative 5t8y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5t8y_X] [5t8y_B] [5t8y_A] [5t8y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5T8Y: [EZ_HEAT ] by SMART
  • Other resources with information on 5T8Y
  • Community annotation for 5T8Y at PDBWiki (http://pdbwiki.org)

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