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- PDB-5d8t: RNA octamer containing (S)-5' methyl, 2'-F U. -

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Basic information

Entry
Database: PDB / ID: 5d8t
TitleRNA octamer containing (S)-5' methyl, 2'-F U.
ComponentsRNA oligonucleotide containing (S)-C5'-Me-2'-FU
KeywordsRNA / modified base
Function / homologyCOBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 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 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 22, 2026Group: Atomic model / Data collection / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_entry_details
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 3.0Aug 12, 2026Group: Derived calculations / Non-polymer description
Category: chem_comp / pdbx_nonpoly_atom_coordination ...chem_comp / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA oligonucleotide containing (S)-C5'-Me-2'-FU
B: RNA oligonucleotide containing (S)-C5'-Me-2'-FU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8876
Polymers5,2432
Non-polymers6444
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-1 kcal/mol
Surface area3160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.172, 31.172, 84.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 2621.475 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.91833 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 24, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91833 Å / Relative weight: 1
ReflectionRedundancy: 14.1 % / Number: 193718 / Rmerge(I) obs: 0.145 / Χ2: 1.09 / D res high: 1.2 Å / D res low: 50 Å / Num. obs: 13758 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
3.265010.0741.02913.1
2.593.2610.0881.07415.2
2.262.5910.1031.25316.4
2.052.2610.1231.25916.5
1.92.0510.1371.15216.7
1.791.910.1571.13216.7
1.71.7910.1681.12316.9
1.631.710.2141.17716.7
1.571.6310.3031.11816.9
1.511.5710.3911.12716.6
1.461.5110.511.08616.4
1.421.4610.5551.03316
1.391.4210.5891.05614.7
1.351.3910.5771.00613
1.321.3510.51.04711.7
1.291.3210.534111.1
1.271.2910.4980.99710.1
1.241.2710.5290.9339.4
1.221.2410.5520.9378.7
1.21.2210.5840.9538.1
ReflectionResolution: 1.2→50 Å / Num. obs: 13758 / % possible obs: 99.7 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 11.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.584 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data collection
HKL-2000data scaling
SHELXphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.2→29.24 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.157 708 5.2 %RANDOM
Rwork0.12 ---
obs0.121 12988 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.2→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 338 28 126 492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d1.8230.015252
X-RAY DIFFRACTIONr_bond_other_d2.8870.018398
X-RAY DIFFRACTIONr_angle_refined_deg42.1961.872303
X-RAY DIFFRACTIONr_angle_other_deg56.8012.52891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr3.6230.221
X-RAY DIFFRACTIONr_gen_planes_refined0.2230.02156
X-RAY DIFFRACTIONr_gen_planes_other0.2960.0268
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4680.927252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr14.6383650
X-RAY DIFFRACTIONr_sphericity_free57.545515
X-RAY DIFFRACTIONr_sphericity_bonded7.6325731
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.161 46 -
Rwork0.14 900 -
obs--98.44 %

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