5D0B Oxidoreductase Rna date Aug 03, 2015
title Crystal Structure Of Epoxyqueuosine Reductase With A Trna-Ty Epoxyqueuosine-Modified Trna Stem Loop
authors D.P.Dowling, Z.D.Miles, C.Kohrer, V.Bandarian, C.L.Drennan
compound source
Molecule: Epoxyqueuosine Reductase
Chain: A, B
Synonym: Queuosine Biosynthesis Protein Queg
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: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pask-Iba43plus

Molecule: Rna (5'-D(Gpcpapgpapcpup(56b) Pupapapapupcpupgpc)-3');
Chain: F
Engineered: Yes

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Other_details: Synthesized By Idt And Enzymatically Modifie
symmetry Space Group: P 1 21 1
R_factor 0.192 R_Free 0.221
length a length b length c angle alpha angle beta angle gamma
45.644 110.754 99.223 90.00 95.16 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand 56B, B12, GOL, PO4, SF4 enzyme Oxidoreductase E.C. BRENDA
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] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (5d0b.pdb1.gz) 72 Kb
  • Biological Unit Coordinates (5d0b.pdb2.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 5D0B
  • CSU: Contacts of Structural Units for 5D0B
  • Structure Factors (137 Kb)
  • Retrieve 5D0B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D0B from S2C, [Save to disk]
  • Re-refined 5d0b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D0B 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 5D0B
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5d0b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d0b_F] [5d0b_A] [5d0b] [5d0b_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D0B: [EZ_HEAT ] by SMART
  • Other resources with information on 5D0B
  • Community annotation for 5D0B at PDBWiki (http://pdbwiki.org)

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