5D0A	Oxidoreductase Rna	date	Aug 03, 2015
title	Crystal Structure Of Epoxyqueuosine Reductase With Cleaved R Loop
authors	D.P.Dowling, Z.D.Miles, C.Kohrer, V.Bandarian, C.L.Drennan
compound		source
Molecule: Epoxyqueuosine Reductase Chain: A, B, C, D 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: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pask-Iba43plus
Molecule: Rna (5'- R(Gcpapgpapcpupgpupapapapupcpupgpc)-3'); Chain: E, F Engineered: Yes		Synthetic: Yes Organism_scientific: Escherichia Coli Organism_taxid: 562 Other_details: Synthesized By Idt
symmetry	Space Group: P 1 21 1	R_factor 0.184 R_Free 0.225
crystal cell	length a length b length c angle alpha angle beta angle gamma 90.587 111.118 96.008 90.00 104.90 90.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	B12, GOL, PO4, SF4	enzyme	Oxidoreductase E.C.1.17.99.6 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Molecular 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] (282 Kb) [Save to disk] Biological Unit Coordinates (5d0a.pdb1.gz) 74 Kb Biological Unit Coordinates (5d0a.pdb2.gz) 74 Kb Biological Unit Coordinates (5d0a.pdb3.gz) 69 Kb Biological Unit Coordinates (5d0a.pdb4.gz) 69 Kb LPC: Ligand-Protein Contacts for 5D0A CSU: Contacts of Structural Units for 5D0A Structure Factors (1145 Kb) Retrieve 5D0A in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5D0A from S2C, [Save to disk] Re-refined 5d0a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D0A 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 5D0A

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5d0a_A] [5d0a_D] [5d0a_E] [5d0a] [5d0a_F] [5d0a_C] [5d0a_B] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5D0A: [EZ_HEAT ] by SMART

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