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- PDB-9okt: 16mer self-complementary duplex RNA with dA:U pair sequence 2 -

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Basic information

Entry
Database: PDB / ID: 9okt
Title16mer self-complementary duplex RNA with dA:U pair sequence 2
ComponentsDNA/RNA (5'-R(*AP*GP*AP*GP*AP*AP*G)-D(P*A)-R(P*UP*CP*UP*UP*CP*UP*CP*U)-3')
KeywordsRNA / Deoxyribo-purine / RNA duplex / Origin of Life
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsFang, Z. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2104708 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Biorxiv / Year: 2025
Title: Impact of 2'-deoxyribo-purine substrates on nonenzymatic RNA template-directed primer extension.
Authors: Fang, Z. / Acikgoz, O. / Jia, X. / Essex, J. / Wen, R. / Szostak, J.W.
History
DepositionMay 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*AP*G)-D(P*A)-R(P*UP*CP*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1404
Polymers5,0671
Non-polymers733
Water1,964109
1
A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*AP*G)-D(P*A)-R(P*UP*CP*UP*UP*CP*UP*CP*U)-3')
hetero molecules

A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*AP*G)-D(P*A)-R(P*UP*CP*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2808
Polymers10,1342
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1850 Å2
ΔGint-35 kcal/mol
Surface area6020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.006, 41.006, 123.438
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

21A-228-

HOH

31A-229-

HOH

41A-266-

HOH

51A-270-

HOH

61A-274-

HOH

71A-287-

HOH

81A-290-

HOH

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*AP*GP*AP*GP*AP*AP*G)-D(P*A)-R(P*UP*CP*UP*UP*CP*UP*CP*U)-3')


Mass: 5067.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.08 M Sodium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 5.5, 35% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.002 M Hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.32→50 Å / Num. obs: 9461 / % possible obs: 96.9 % / Redundancy: 9.4 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.021 / Rrim(I) all: 0.064 / Χ2: 0.928 / Net I/σ(I): 30.3
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 4 / Num. unique obs: 417 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.18 / Rrim(I) all: 0.543 / Χ2: 0.884 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→34.128 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.979 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2065 438 4.681 %
Rwork0.1828 8918 -
all0.184 --
obs-9356 95.792 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20.001 Å20 Å2
2--0.002 Å20 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.32→34.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 335 3 109 447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011374
X-RAY DIFFRACTIONr_bond_other_d0.0020.018156
X-RAY DIFFRACTIONr_angle_refined_deg2.2971.837580
X-RAY DIFFRACTIONr_angle_other_deg0.6941.643381
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.069511
X-RAY DIFFRACTIONr_chiral_restr0.0910.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.02185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0259
X-RAY DIFFRACTIONr_nbd_refined0.0920.238
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.2154
X-RAY DIFFRACTIONr_nbtor_refined0.2550.2136
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.267
X-RAY DIFFRACTIONr_metal_ion_refined0.080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0870.214
X-RAY DIFFRACTIONr_nbd_other0.1430.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1550.251
X-RAY DIFFRACTIONr_scbond_it1.2971.357374
X-RAY DIFFRACTIONr_scbond_other1.2951.355375
X-RAY DIFFRACTIONr_scangle_it1.8152.48580
X-RAY DIFFRACTIONr_scangle_other1.8132.479581
X-RAY DIFFRACTIONr_lrange_it5.30624.793557
X-RAY DIFFRACTIONr_lrange_other4.65419.901515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.32-1.3540.39200.2745070.2776910.9270.95276.26630.247
1.354-1.3910.284320.2456080.2476940.9420.95992.2190.221
1.391-1.4310.292360.2415950.2446640.940.96295.03010.211
1.431-1.4750.313260.2346110.2376590.9310.96796.66160.206
1.475-1.5240.199260.2085880.2076350.9760.97396.69290.185
1.524-1.5770.214450.1775520.186140.9710.97997.23130.162
1.577-1.6360.146240.185530.1795940.9880.9897.1380.171
1.636-1.7030.228340.185300.1835790.9660.98197.40930.169
1.703-1.7780.202250.1665150.1675520.9760.98297.82610.166
1.778-1.8650.172140.1824980.1825230.9840.97897.89680.188
1.865-1.9660.247280.24680.2035060.970.97398.02370.206
1.966-2.0840.24210.1784480.1814760.960.97998.52940.19
2.084-2.2280.247200.1864190.1884450.9710.97898.65170.203
2.228-2.4050.21190.1784090.1794330.9760.98198.84530.2
2.405-2.6340.146180.1893650.1873870.9890.97898.96640.224
2.634-2.9420.342120.1853420.193570.9460.97799.15970.227
2.942-3.3930.162140.1693010.1693200.980.98798.43750.229
3.393-4.1460.08350.1532630.1512720.990.98798.52940.209
4.146-5.820.122110.1362100.1352210.9930.9881000.2
5.82-34.1280.30880.221360.2241440.9580.9711000.287

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