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- PDB-5der: RNA oligonucleotide containing (R)-C5'-ME-2'F U -

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Basic information

Entry
Database: PDB / ID: 5der
TitleRNA oligonucleotide containing (R)-C5'-ME-2'F U
ComponentsRNA oligonucleotide containing (R)-C5'-Me-2'-FU
KeywordsRNA / oligonucleotide
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsHarp, J.M. / Egli, M.
CitationJournal: J.Org.Chem. / Year: 2016
Title: Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides.
Authors: Kel In, A.V. / Zlatev, I. / Harp, J. / Jayaraman, M. / Bisbe, A. / O Shea, J. / Taneja, N. / Manoharan, R.M. / Khan, S. / Charisse, K. / Maier, M.A. / Egli, M. / Rajeev, K.G. / Manoharan, M.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA oligonucleotide containing (R)-C5'-Me-2'-FU
B: RNA oligonucleotide containing (R)-C5'-Me-2'-FU
C: RNA oligonucleotide containing (R)-C5'-Me-2'-FU
D: RNA oligonucleotide containing (R)-C5'-Me-2'-FU


Theoretical massNumber of molelcules
Total (without water)10,1704
Polymers10,1704
Non-polymers00
Water3,495194
1
A: RNA oligonucleotide containing (R)-C5'-Me-2'-FU
B: RNA oligonucleotide containing (R)-C5'-Me-2'-FU


Theoretical massNumber of molelcules
Total (without water)5,0852
Polymers5,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint1 kcal/mol
Surface area3110 Å2
MethodPISA
2
C: RNA oligonucleotide containing (R)-C5'-Me-2'-FU
D: RNA oligonucleotide containing (R)-C5'-Me-2'-FU


Theoretical massNumber of molelcules
Total (without water)5,0852
Polymers5,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint1 kcal/mol
Surface area3110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.116, 44.116, 86.927
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-228-

HOH

21D-317-

HOH

31D-351-

HOH

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Components

#1: RNA chain
RNA oligonucleotide containing (R)-C5'-Me-2'-FU


Mass: 2542.579 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 40.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 12 mM NaCl, 80 mM KCl, reservoir 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 30, 2014 / Details: Montel multilayer, confocal mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→25.34 Å / Num. obs: 15381 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.57
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2.73 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.77 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PROTEUM PLUSdata collection
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIX1.9_1692phasing
RefinementResolution: 1.8→25.34 Å / Cross valid method: FREE R-VALUE / σ(F): 0.143 / Phase error: 31.818088423
RfactorNum. reflection% reflection
Rfree0.274 454 5.39753935706 %
Rwork0.257 14302 -
obs0.248 15118 99.6375140051 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.4012714523 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 672 0 194 866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419357466461748
X-RAY DIFFRACTIONf_angle_d0.856316658951160
X-RAY DIFFRACTIONf_chiral_restr0.0335223668827160
X-RAY DIFFRACTIONf_plane_restr0.0018455296403232
X-RAY DIFFRACTIONf_dihedral_angle_d15.1239428142444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8041-1.9170.3528517482461590.3266237802612369X-RAY DIFFRACTION93.341213554
1.917-2.06480.2869112944451440.2900125857572363X-RAY DIFFRACTION94.2560829677
2.0648-2.27220.3043690525541310.2698081161722379X-RAY DIFFRACTION94.7054140127
2.2722-2.60010.2684015874351150.2778541734222404X-RAY DIFFRACTION95.4346963081
2.6001-3.27240.2181496533461440.2384688551632359X-RAY DIFFRACTION94.1716566866
3.2724-17.55190.2473755723121230.1992875785272376X-RAY DIFFRACTION94.5859872611

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