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- PDB-5u0q: RNA-DNA heptamer duplex with one 2'-5'-linkage -

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Basic information

Entry
Database: PDB / ID: 5u0q
TitleRNA-DNA heptamer duplex with one 2'-5'-linkage
Components
  • DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')
  • RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
KeywordsRNA / DNA / 2'-5'-LINKAGE / RNA-DNA
Function / homology: / DNA/RNA hybrid / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsLuo, Z. / Sheng, J.
CitationJournal: To Be Published
Title: RNA-DNA heptamer duplex with one 2'-5'-linkage
Authors: Luo, Z. / Sheng, J. / Wang, R.
History
DepositionNov 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Mar 28, 2018Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Oct 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(*UP*AP*GP*CP*UP*CP*C)-3')
B: DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')
C: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
D: DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9638
Polymers8,8324
Non-polymers1324
Water2,126118
1
A: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
B: DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4403
Polymers4,4162
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-4 kcal/mol
Surface area2790 Å2
MethodPISA
2
C: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
D: DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5235
Polymers4,4162
Non-polymers1083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-20 kcal/mol
Surface area3000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.554, 52.923, 27.622
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2157.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA/RNA hybrid DNA/RNA (5'-R(*GP*GP*AP*GP*C)-D(P*T)-R(P*A)-3')


Mass: 2258.446 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040 M Sodium cacodylate trihydrate pH 5.5, 0.020 M Hexamine cobalt(III) chloride, 0.02 M Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 14036 / % possible obs: 98.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.6
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKO

5tko


Resolution: 1.43→18.11 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 3.572 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17692 662 4.7 %RANDOM
Rwork0.15269 ---
obs0.15376 13355 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.656 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å2-0 Å2-1.16 Å2
2---1.49 Å2-0 Å2
3----1.64 Å2
Refinement stepCycle: 1 / Resolution: 1.43→18.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 584 4 118 706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.011650
X-RAY DIFFRACTIONr_bond_other_d0.0050.02286
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.261998
X-RAY DIFFRACTIONr_angle_other_deg5.5763684
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_restr0.1140.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02330
X-RAY DIFFRACTIONr_gen_planes_other0.010.02144
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_it3.4184.646650
X-RAY DIFFRACTIONr_scbond_other3.4164.646651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7348.807999
X-RAY DIFFRACTIONr_long_range_B_refined5.60121.568979
X-RAY DIFFRACTIONr_long_range_B_other5.5621.513976
X-RAY DIFFRACTIONr_rigid_bond_restr4.2853936
X-RAY DIFFRACTIONr_sphericity_free36.362564
X-RAY DIFFRACTIONr_sphericity_bonded19.7325928
LS refinement shellResolution: 1.426→1.503 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.239 85 -
Rwork0.255 1915 -
obs--97.47 %

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