5E54 Rna date Oct 07, 2015
title Two Apo Structures Of The Adenine Riboswitch Aptamer Domain Using An X-Ray Free Electron Laser
authors J.R.Stagno, Y.X.Wang, Y.Liu, Y.R.Bhandari, C.E.Conrad, G.Nelson, D.R.Wendel, T.A.White, A.Barty, R.A.Tuckey, N.A.Zatsepin, T.D.Gr P.Fromme, K.Tan, X.Ji, J.C.H.Spence
compound source
Molecule: Vibrio Vulnificus Strain 93u204 Chromosome II, Ad Riboswitch Aptamer Domain;
Chain: A, B
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Vibrio Vulnificus
Organism_taxid: 672
symmetry Space Group: P 1 21 1
R_factor 0.213 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.910 46.720 92.250 90.00 94.06 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand MG enzyme
Primary referenceStructures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography., Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferre-D'Amare AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA, Wang YX, Nature. 2016 Nov 14. doi: 10.1038/nature20599. PMID:27841871
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (120 Kb) [Save to disk]
  • Biological Unit Coordinates (5e54.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (5e54.pdb2.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 5E54
  • CSU: Contacts of Structural Units for 5E54
  • Structure Factors (391 Kb)
  • Retrieve 5E54 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5E54 from S2C, [Save to disk]
  • Re-refined 5e54 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5E54 in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5E54
  • 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: [5e54_A] [5e54] [5e54_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5E54
  • Community annotation for 5E54 at PDBWiki (http://pdbwiki.org)

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