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- PDB-9okv: 16mer self-complementary duplex RNA with dA:s(2)U pair sequence 2 -

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Basic information

Entry
Database: PDB / ID: 9okv
Title16mer self-complementary duplex RNA with dA:s(2)U pair sequence 2
ComponentsDNA/RNA (5'-R(*AP*GP*AP*GP*AP*AP*G)-D(P*A)-R(P*(SUR)P*CP*UP*UP*CP*UP*CP*U)-3')
KeywordsRNA / Deoxyribo-purine / 2-thiouridine / 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: 1.233 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*(SUR)P*CP*UP*UP*CP*UP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,0831
Polymers5,0831
Non-polymers00
Water1,928107
1
A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*AP*G)-D(P*A)-R(P*(SUR)P*CP*UP*UP*CP*UP*CP*U)-3')

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


Theoretical massNumber of molelcules
Total (without water)10,1662
Polymers10,1662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2690 Å2
ΔGint1 kcal/mol
Surface area5550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.147, 41.147, 124.373
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-108-

HOH

21A-124-

HOH

31A-163-

HOH

41A-188-

HOH

51A-194-

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*(SUR)P*CP*UP*UP*CP*UP*CP*U)-3')


Mass: 5083.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.02 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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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: Oct 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 11714 / % possible obs: 96.2 % / Redundancy: 8.3 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.014 / Rrim(I) all: 0.043 / Χ2: 0.91 / Net I/σ(I): 52
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 388 / CC1/2: 0.945 / CC star: 0.986 / Rpim(I) all: 0.127 / Rrim(I) all: 0.251 / Χ2: 0.976 / % possible all: 62.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.233→41.458 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.785 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2273 586 5.054 %
Rwork0.1834 11009 -
all0.185 --
obs-11595 95.771 %
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: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0.002 Å2-0 Å2
2---0.003 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.233→41.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 335 0 107 442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.012372
X-RAY DIFFRACTIONr_bond_other_d0.0250.019157
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.89572
X-RAY DIFFRACTIONr_angle_other_deg0.8281.771384
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.059511
X-RAY DIFFRACTIONr_chiral_restr0.0840.276
X-RAY DIFFRACTIONr_chiral_restr_other0.220.22
X-RAY DIFFRACTIONr_gen_planes_refined0.030.02185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0259
X-RAY DIFFRACTIONr_nbd_refined0.420.247
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2760.2166
X-RAY DIFFRACTIONr_nbtor_refined0.2420.2149
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.295
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2950.299
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0820.214
X-RAY DIFFRACTIONr_nbd_other0.130.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.248
X-RAY DIFFRACTIONr_scbond_it1.1341.411372
X-RAY DIFFRACTIONr_scbond_other1.1331.41373
X-RAY DIFFRACTIONr_scangle_it1.5672.564572
X-RAY DIFFRACTIONr_scangle_other1.5662.562573
X-RAY DIFFRACTIONr_lrange_it5.83125.251606
X-RAY DIFFRACTIONr_lrange_other4.89820.698545
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
1.233-1.2650.282260.2645050.2658620.9390.95361.60090.233
1.265-1.2990.348410.2416910.2468730.9410.96283.84880.209
1.299-1.3370.288370.2337550.2358270.9540.96595.76780.202
1.337-1.3780.262420.2367710.2388130.9530.9631000.205
1.378-1.4230.351440.2127380.2187820.9260.9711000.187
1.423-1.4730.287540.2057150.217690.9560.9731000.185
1.473-1.5290.237390.2056880.2077280.9670.97499.86260.19
1.529-1.5910.244260.1716860.1737120.9660.9811000.167
1.591-1.6620.223350.1816420.1836770.9570.9811000.184
1.662-1.7420.234310.1846160.1866470.970.981000.191
1.742-1.8370.193270.1866140.1876410.9740.9781000.198
1.837-1.9480.244180.2035660.2045840.9710.9741000.221
1.948-2.0820.231360.1895260.1915620.9620.9771000.215
2.082-2.2480.155190.2055040.2035230.9820.9731000.238
2.248-2.4620.29240.1924570.1964810.9560.9771000.23
2.462-2.7510.212250.1834220.1854470.9740.981000.235
2.751-3.1750.193220.1693730.1713960.9770.98499.74750.23
3.175-3.8830.182150.1393150.143330.9780.98999.09910.213
3.883-5.4670.248180.1432600.1482780.9650.9881000.209
5.467-41.4580.14370.2051650.2021720.9860.9731000.311

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