5E54

Two apo structures of the adenine riboswitch aptamer domain determined using an X-ray free electron laser

> Summary

Summary for 5E54

DescriptorVibrio vulnificus strain 93U204 chromosome II, complete sequence
Functional Keywordsadenine riboswitch, purine riboswitch, apo, ligand-free, rna, gene regulation, x-ray free electron laser
Biological sourceVibrio vulnificus
Total number of polymer chains2
Total molecular weight45471.99
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 (2.3 Å)
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Structure validation

RfreeClashscoreRSRZ outliersRNA backbone0.254212.8%0.57MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5e54
no rotation
Molmil generated image of 5e54
rotated about x axis by 90°
Molmil generated image of 5e54
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5e54
no rotation
Molmil generated image of 5e54
rotated about x axis by 90°
Molmil generated image of 5e54
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 (5e54.pdb1.gz [59.05 KB])
Coordinate files for Biological unit (5e54.pdb2.gz [61.99 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
MAGNESIUM IONnon-polymer24.34
waterwater18.014

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight45374.8
Non-Polymers*Number of molecules4
Total molecular weight97.2
All*Total molecular weight45472.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.3 Å)

Cell axes47.91046.72092.250
Cell angles90.0094.0690.00
SpacegroupP 1 21 1
Resolution limits25.02 - 2.30
the highest resolution shell value2.359 - 2.300
R-factor0.2156
R-work0.21310
the highest resolution shell value0.640
R-free0.25620
the highest resolution shell value0.660
RMSD bond length0.007
RMSD bond angle1.619

Data Collection Statistics

Resolution limits25.02 - 2.30
the highest resolution shell value -
Number of reflections18602
Completeness100.0
Redundancy461.3
the highest resolution shell value314.6

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 MG A 101
ChainResidue
AG37
AHOH201
AHOH204
BU68
BHOH206
BHOH209

AC27binding site for residue MG A 102
ChainResidue
AU51
AA52
AHOH202
AHOH203
BHOH203
BHOH205
BHOH208

AC33binding site for residue MG A 103
ChainResidue
AU22
AA23
AU48

AC44binding site for residue MG B 101
ChainResidue
BA24
BHOH201
BHOH202
BHOH207

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

site_idNumber of ResiduesDetails
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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

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5e54.ent.gz (122.54 KB)
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all (no-compress)pdb5e54.ent (481.1 KB)
header onlypdb5e54.ent.gz (5 KB)
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PDBx/mmCIF5e54.cif.gz (152.6 KB)
PDBMLall5e54.xml.gz (200.13 KB)
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no-atom5e54-noatom.xml.gz (23.82 KB)
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ext-atom5e54-extatom.xml.gz (63.15 KB)
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PDBMLplusall5e54-plus.xml.gz (200.35 KB)
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no-atom5e54-plus-noatom.xml.gz (24.04 KB)
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add only5e54-add.xml.gz (225 B)
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RDF5e54.rdf.gz (38.95 KB)
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Structure factorsr5e54sf.ent.gz (391.38 KB)
Biological unit (PDB format)5e54.pdb1.gz (59.05 KB) (A)
*author and software defined assembly, 1 molecule(s) (monomeric)
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5e54.pdb2.gz (61.99 KB) (B)
*author and software defined assembly, 1 molecule(s) (monomeric)
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Validation reportsPDF5e54​_validation.pdf.gz (395.3 KB)
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PDF-full5e54​_full​_validation.pdf.gz (397.56 KB)
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XML5e54​_validation.xml.gz (6 KB)
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PNG5e54​_multipercentile​_validation.png.gz (121.68 KB)
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SVG5e54​_multipercentile​_validation.svg.gz (889 B)
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Sequence (fasta)5e54​_seq.txt
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