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 Diffraction	resolution	2.65 Å
ligand	B12, PO4, SF4	enzyme	Oxidoreductase E.C.1.17.99.6 BRENDA
Gene Ontology	Chain Function Process Component A, 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] (130 Kb) [Save to disk] Biological Unit Coordinates (5t8y.pdb1.gz) 62 Kb Biological Unit Coordinates (5t8y.pdb2.gz) 64 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

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: [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)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---