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- PDB-7ooo: The crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCT... -

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Basic information

Entry
Database: PDB / ID: 7ooo
TitleThe crystal structure of a DNA:RNA hybrid duplex sequence CTTTTCTTTG containing an LNA-Amide-LNA modification
Components
  • DNA (5'-D(*CP*TP*(05A)P*TP*CP*TP*TP*TP*G)-3')
  • RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
KeywordsDNA-RNA HYBRID / Amide-LNA / duplex / DNA:RNA / DNA:RNA HYBRID
Function / homologyDNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsThorpe, C. / Hardwick, J. / McDonough, M.A. / Hall, J.P. / Baker, Y.R. / El-Sagheer, A.H. / Brown, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S018794/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: An LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides.
Authors: Baker, Y.R. / Thorpe, C. / Chen, J. / Poller, L.M. / Cox, L. / Kumar, P. / Lim, W.F. / Lie, L. / McClorey, G. / Epple, S. / Singleton, D. / McDonough, M.A. / Hardwick, J.S. / Christensen, K. ...Authors: Baker, Y.R. / Thorpe, C. / Chen, J. / Poller, L.M. / Cox, L. / Kumar, P. / Lim, W.F. / Lie, L. / McClorey, G. / Epple, S. / Singleton, D. / McDonough, M.A. / Hardwick, J.S. / Christensen, K.E. / Wood, M.J.A. / Hall, J.P. / El-Sagheer, A.H. / Brown, T.
History
DepositionMay 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 2.0Mar 15, 2023Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*(05A)P*TP*CP*TP*TP*TP*G)-3')
D: RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
E: DNA (5'-D(*CP*TP*(05A)P*TP*CP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5776
Polymers12,5284
Non-polymers492
Water181
1
A: RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*(05A)P*TP*CP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2883
Polymers6,2642
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')
E: DNA (5'-D(*CP*TP*(05A)P*TP*CP*TP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2883
Polymers6,2642
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.150, 49.150, 90.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-101-

MG

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Components

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


Mass: 3255.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*TP*(05A)P*TP*CP*TP*TP*TP*G)-3')


Mass: 3009.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Drop solution 0.5 mM duplex, 40 mM Sodium chloride, 6.0 mM Potassium chloride, 20 mM Sodium cacodylate trihydrate pH 6.0, 15% (v/v) MPD, 6.0 mM Spermine tetrahydrochloride; Well solution ...Details: Drop solution 0.5 mM duplex, 40 mM Sodium chloride, 6.0 mM Potassium chloride, 20 mM Sodium cacodylate trihydrate pH 6.0, 15% (v/v) MPD, 6.0 mM Spermine tetrahydrochloride; Well solution Component concentrations are double the concentration of the drop solution and do not contain the oligonucleotide duplex

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.56→31.08 Å / Num. obs: 4398 / % possible obs: 99.4 % / Redundancy: 18.7 % / CC1/2: 0.999 / Net I/σ(I): 19.8
Reflection shellResolution: 2.56→2.63 Å / Num. unique obs: 309 / CC1/2: 0.329

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NRP

7nrp


Resolution: 2.57→31.08 Å / SU ML: 0 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 208 4.78 %
Rwork0.2326 --
obs0.2333 4349 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 834 2 1 837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007932
X-RAY DIFFRACTIONf_angle_d1.8891442
X-RAY DIFFRACTIONf_dihedral_angle_d14.536434
X-RAY DIFFRACTIONf_chiral_restr0.095176
X-RAY DIFFRACTIONf_plane_restr0.00542
LS refinement shellResolution: 2.57→31.08 Å
RfactorNum. reflection% reflection
Rfree0.2513 208 -
Rwork0.2326 4141 -
obs--99 %

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