5SWD

Structure of the adenine riboswitch aptamer domain in an intermediate-bound state

Summary for 5SWD

Related5E54 5SWE
DescriptorVibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain, ADENINE, MAGNESIUM ION, ... (4 entities in total)
Functional Keywordsadenine riboswitch, purine riboswitch, ligand mixing, intermediate state, rna, gene regulation, x-ray free electron laser
Biological sourceVibrio vulnificus
Total number of polymer chains2
Total molecular weight45582.81
Authors
Primary citation
Stagno, J.R.,Liu, Y.,Bhandari, Y.R.,Conrad, C.E.,Panja, S.,Swain, M.,Fan, L.,Nelson, G.,Li, C.,Wendel, D.R.,White, T.A.,Coe, J.D.,Wiedorn, M.O.,Knoska, J.,Oberthuer, D.,Tuckey, R.A.,Yu, P.,Dyba, M.,Tarasov, S.G.,Weierstall, U.,Grant, T.D.,Schwieters, C.D.,Zhang, J.,Ferre-D'Amare, A.R.,Fromme, P.,Draper, D.E.,Liang, M.,Hunter, M.S.,Boutet, S.,Tan, K.,Zuo, X.,Ji, X.,Barty, A.,Zatsepin, N.A.,Chapman, H.N.,Spence, J.C.,Woodson, S.A.,Wang, Y.X.
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.
Nature, 541:242-246, 2017
PubMed: 27841871 (PDB entries with the same primary citation)
DOI: 10.1038/nature20599
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.5 Å)
?

Structure validation

RfreeClashscoreRSRZ outliersRNA backbone0.230115.3%0.54MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5swd
no rotation
Molmil generated image of 5swd
rotated about x axis by 90°
Molmil generated image of 5swd
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5swd
no rotation
Molmil generated image of 5swd
rotated about x axis by 90°
Molmil generated image of 5swd
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5swd.pdb1.gz [61.63 KB])
Coordinate files for Biological unit (5swd.pdb2.gz [62.24 KB])
PDBj@FacebookPDBj@TwitterwwPDBwwPDB Foundation

Copyright © 2013-2018 Protein Data Bank Japan