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- PDB-9oku: 16mer self-complementary duplex RNA with dA:s(2)U pair sequence 1 -

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Basic information

Entry
Database: PDB / ID: 9oku
Title16mer self-complementary duplex RNA with dA:s(2)U pair sequence 1
ComponentsDNA/RNA (5'-R(*AP*GP*AP*G)-D(P*A)-R(P*AP*GP*AP*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: 1.479 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*G)-D(P*A)-R(P*AP*GP*AP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1072
Polymers5,0831
Non-polymers241
Water1,820101
1
A: DNA/RNA (5'-R(*AP*GP*AP*G)-D(P*A)-R(P*AP*GP*AP*UP*CP*U)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,2154
Polymers10,1662
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2680 Å2
ΔGint-12 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.167, 41.167, 124.563
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-218-

HOH

21A-250-

HOH

31A-268-

HOH

41A-276-

HOH

51A-286-

HOH

61A-288-

HOH

71A-292-

HOH

81A-301-

HOH

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Components

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


Mass: 5083.130 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.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 38.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, 30% v/v Polyethylene glycol 400

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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: 1.479→50 Å / Num. obs: 7122 / % possible obs: 100 % / Redundancy: 9.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.022 / Rrim(I) all: 0.065 / Χ2: 0.982 / Net I/σ(I): 33
Reflection shellResolution: 1.479→1.51 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 344 / CC1/2: 0.901 / CC star: 0.974 / Rpim(I) all: 0.204 / Rrim(I) all: 0.609 / Χ2: 0.931 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.479→41.521 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.38 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2115 348 4.895 %
Rwork0.1697 6761 -
all0.172 --
obs-7109 99.789 %
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: 11.489 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.479→41.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 335 1 101 437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012374
X-RAY DIFFRACTIONr_bond_other_d0.0290.019159
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.89572
X-RAY DIFFRACTIONr_angle_other_deg2.6991.778386
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.083511
X-RAY DIFFRACTIONr_chiral_restr0.0780.276
X-RAY DIFFRACTIONr_chiral_restr_other2.4010.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0270.02185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0259
X-RAY DIFFRACTIONr_nbd_refined0.1130.236
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.2164
X-RAY DIFFRACTIONr_nbtor_refined0.2490.2137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.268
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.080.211
X-RAY DIFFRACTIONr_nbd_other0.1430.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.250
X-RAY DIFFRACTIONr_scbond_it1.281.282374
X-RAY DIFFRACTIONr_scbond_other1.2781.28375
X-RAY DIFFRACTIONr_scangle_it1.8712.337572
X-RAY DIFFRACTIONr_scangle_other1.8692.335573
X-RAY DIFFRACTIONr_lrange_it5.93422.51558
X-RAY DIFFRACTIONr_lrange_other5.4218.708519
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
1.479-1.5170.312230.2674850.2695130.9530.95399.02530.232
1.517-1.5590.352250.2144740.224990.9330.9671000.179
1.559-1.6040.22210.1984730.1994940.9750.9731000.174
1.604-1.6530.219230.1894520.1914750.9670.9771000.173
1.653-1.7070.224340.1844350.1874690.9590.981000.168
1.707-1.7670.235120.1784240.184360.9680.981000.163
1.767-1.8340.191210.1614090.1624300.9730.9831000.15
1.834-1.9080.221150.1913970.1924150.970.97699.27710.163
1.908-1.9930.224260.23840.2024120.9710.97499.51460.184
1.993-2.090.245140.173680.1733820.9770.981000.166
2.09-2.2030.278170.1813390.1863560.9690.9791000.176
2.203-2.3360.289150.2063350.2093540.960.97698.87010.207
2.336-2.4970.274230.1873000.1933230.9620.9791000.196
2.497-2.6960.212160.1942960.1953120.9710.9771000.205
2.696-2.9520.24170.1552730.1592900.9660.9851000.177
2.952-3.2990.155100.132480.1312590.9860.99199.61390.172
3.299-3.8050.12990.132240.132330.9930.9911000.167
3.805-4.650.164120.121920.1232040.9830.9921000.167
4.65-6.5360.18690.1461540.1481630.980.9881000.206
6.536-41.5210.11660.1631010.161070.9950.9811000.254

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