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- PDB-5vr4: RNA octamer containing 2'-F-4'-OMe U. -

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Basic information

Entry
Database: PDB / ID: 5vr4
TitleRNA octamer containing 2'-F-4'-OMe U.
ComponentsRNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
KeywordsRNA
Function / homologyCOBALT TETRAAMMINE ION / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHarp, J.M. / Egli, M.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: 4'-C-Methoxy-2'-deoxy-2'-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing.
Authors: Malek-Adamian, E. / Guenther, D.C. / Matsuda, S. / Martinez-Montero, S. / Zlatev, I. / Harp, J. / Burai Patrascu, M. / Foster, D.J. / Fakhoury, J. / Perkins, L. / Moitessier, N. / Manoharan, ...Authors: Malek-Adamian, E. / Guenther, D.C. / Matsuda, S. / Martinez-Montero, S. / Zlatev, I. / Harp, J. / Burai Patrascu, M. / Foster, D.J. / Fakhoury, J. / Perkins, L. / Moitessier, N. / Manoharan, R.M. / Taneja, N. / Bisbe, A. / Charisse, K. / Maier, M. / Rajeev, K.G. / Egli, M. / Manoharan, M. / Damha, M.J.
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
B: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
C: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
D: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3615
Polymers10,2344
Non-polymers1271
Water2,468137
1
A: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
B: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,1172
Polymers5,1172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
D: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2443
Polymers5,1172
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.387, 44.387, 85.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

21B-333-

HOH

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Components

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


Mass: 2558.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CON / COBALT TETRAAMMINE ION


Mass: 127.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH12N4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.08 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.5 mM RNA, 10 mM Cobalt(III) hexamine, 6 mM sodium chloride, 40 mM potassium chloride, 5% MPD, 20 mM sodium cacodylate equilibrated against reservoir containing 40% MPD
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 26152 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Net I/σ(I): 21.05
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.73 / CC1/2: 0.943 / Rpim(I) all: 0.317 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P4A

3p4a


Resolution: 1.5→29.481 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.2425 1375 5.26 %
Rwork0.1861 --
obs0.189 26152 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 676 3 137 816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009754
X-RAY DIFFRACTIONf_angle_d1.8041169
X-RAY DIFFRACTIONf_dihedral_angle_d8.223336
X-RAY DIFFRACTIONf_chiral_restr0.072152
X-RAY DIFFRACTIONf_plane_restr0.03736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4971-1.55060.321330.24482452X-RAY DIFFRACTION98
1.5506-1.61270.25981420.21012481X-RAY DIFFRACTION99
1.6127-1.6860.25141330.19742495X-RAY DIFFRACTION99
1.686-1.77490.26311080.17032518X-RAY DIFFRACTION99
1.7749-1.88610.20391560.17182444X-RAY DIFFRACTION100
1.8861-2.03170.22041590.17162503X-RAY DIFFRACTION100
2.0317-2.23610.26921480.17082482X-RAY DIFFRACTION100
2.2361-2.55950.26791240.19322495X-RAY DIFFRACTION100
2.5595-3.22410.24151510.18972473X-RAY DIFFRACTION99
3.2241-29.48670.22561210.18642434X-RAY DIFFRACTION97

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