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- PDB-6cy0: RNA octamer containing 2'-F, 4'-Cbeta-OMe U. -

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Basic information

Entry
Database: PDB / ID: 6cy0
TitleRNA octamer containing 2'-F, 4'-Cbeta-OMe U.
ComponentsRNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
KeywordsRNA / oligonucleotide / modified base
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.398 Å
AuthorsHarp, J.M. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity.
Authors: Harp, J.M. / Guenther, D.C. / Bisbe, A. / Perkins, L. / Matsuda, S. / Bommineni, G.R. / Zlatev, I. / Foster, D.J. / Taneja, N. / Charisse, K. / Maier, M.A. / Rajeev, K.G. / Manoharan, M. / Egli, M.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
B: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
C: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
D: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
E: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
F: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
G: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
H: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)21,1008
Polymers21,1008
Non-polymers00
Water3,153175
1
A: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
B: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2752
Polymers5,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
D: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2752
Polymers5,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
F: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2752
Polymers5,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')
H: RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,2752
Polymers5,2752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.012, 47.631, 100.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain
RNA (5'-R(*(CBV)P*GP*AP*AP*(UFB)P*UP*CP*G)-3')


Mass: 2637.474 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 mM RNA; 100 mM MES, 2.5 M ammonium sulfate, 10 mM magnesium chloride,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.398→42.602 Å / Num. obs: 9164 / % possible obs: 97.4 % / Redundancy: 21.6 % / CC1/2: 0.991 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.058 / Net I/σ(I): 11
Reflection shellResolution: 2.398→2.49 Å / Rmerge(I) obs: 0.433 / Num. unique obs: 907 / CC1/2: 0.995 / Rpim(I) all: 0.129

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Processing

Software
NameVersionClassification
PHENIX1.13_2992refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.398→42.602 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.93 / Phase error: 23.47
RfactorNum. reflection% reflection
Rfree0.2423 855 5.12 %
Rwork0.2023 --
obs0.2043 16693 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.34 Å2 / Biso mean: 17.7757 Å2 / Biso min: 2.4 Å2
Refinement stepCycle: final / Resolution: 2.398→42.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1360 0 175 1535
Biso mean---23.71 -
Num. residues----64
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3978-2.5480.28351750.23812509268495
2.548-2.74470.28521320.23912672280498
2.7447-3.02080.2551190.247827392858100
3.0208-3.45780.24931550.18962604275997
3.4578-4.35570.20341540.17942662281699
4.3557-42.60880.22361200.172652277297

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