5SWD

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

> Summary

Summary for 5SWD

Related5E54 5SWE
DescriptorVibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domain
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
DOI: 10.1038/nature20599
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.5 Å)
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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])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BVibrio vulnificus strain 93U204 chromosome II, adenine riboswitch aptamer domainpolymer7122687.42
Vibrio vulnificus
ADENINEnon-polymer135.11
MAGNESIUM IONnon-polymer24.33
waterwater18.015

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight45374.8
Non-Polymers*Number of molecules4
Total molecular weight208.0
All*Total molecular weight45582.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.5 Å)

Cell axes47.91046.72092.250
Cell angles90.0094.0690.00
SpacegroupP 1 21 1
Resolution limits30.92 - 2.50
the highest resolution shell value2.568 - 2.503
R-factor0.1969
R-work0.19490
the highest resolution shell value0.548
R-free0.22940
the highest resolution shell value0.735
RMSD bond length0.007
RMSD bond angle1.524

Data Collection Statistics

Resolution limits31.06 - 2.50
the highest resolution shell value -
Number of reflections14357
Completeness100.0
Redundancy346.8
the highest resolution shell value188.3

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
AC17binding site for residue ADE A 101
ChainResidue
AA21
AU22
AU48
AU49
AA73
AU74
AHOH204

AC26binding site for residue MG A 102
ChainResidue
AG37
AHOH205
AHOH206
BU68
BHOH204
BHOH207

AC37binding site for residue MG A 103
ChainResidue
AU51
AA52
AHOH201
AHOH207
BHOH205
BHOH206
BHOH208

AC44binding site for residue MG B 101
ChainResidue
BA24
BHOH201
BHOH202
BHOH203

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

site_idNumber of ResiduesDetails
ADE_5swd_A_1019ADENINE binding site
ChainResidueligand
AA21-A24ADE: ADENINE
AU48-U49ADE: ADENINE
AA73-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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