5SWE

Ligand-bound structure of adenine riboswitch aptamer domain converted in crystal from its ligand-free state using ligand mixing serial femtosecond crystallography

> Summary

Summary for 5SWE

Related5E54 5SWD
DescriptorVibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
Functional Keywordsadenine riboswitch, purine riboswitch, ligand mixing, rna, gene regulation, x-ray free electron laser
Biological sourceVibrio vulnificus
Total number of polymer chains1
Total molecular weight22822.51
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
DOI: 10.1038/nature20599
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3 Å)
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Structure validation

RfreeClashscoreRSRZ outliersRNA backbone0.374142.8%0.44MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
XVibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domainpolymer7122687.41
Vibrio vulnificus
ADENINEnon-polymer135.11

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight22687.4
Non-Polymers*Number of molecules1
Total molecular weight135.1
All*Total molecular weight22822.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3 Å)

Cell axes49.900154.90025.200
Cell angles90.0090.0090.00
SpacegroupP 21 21 2
Resolution limits26.32 - 3.00
the highest resolution shell value3.077 - 3.000
R-factor0.3503
R-work0.34890
the highest resolution shell value0.421
R-free0.37900
the highest resolution shell value0.407
RMSD bond length0.003
RMSD bond angle0.856

Data Collection Statistics

Resolution limits26.32 - 3.00
the highest resolution shell value -
Number of reflections4115
Completeness95.0
Redundancy20.3
the highest resolution shell value13

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1BATCH MODE6.5295

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16binding site for residue ADE X 101
ChainResidue
XA21
XU22
XU47
XU51
XA52
XU75

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
ADE_5swe_X_1019ADENINE binding site
ChainResidueligand
XA21-U22ADE: ADENINE
XU47ADE: ADENINE
XC50-A52ADE: ADENINE
XA73-U75ADE: ADENINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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