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- PDB-9okz: 16mer self-complementary duplex RNA with dG:s(2)C pair sequence 2 -

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Basic information

Entry
Database: PDB / ID: 9okz
Title16mer self-complementary duplex RNA with dG:s(2)C pair sequence 2
ComponentsDNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
KeywordsRNA / Deoxyribo-purine / 2-thiocytidine / RNA duplex / Origin of Life
Function / homology: / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.919 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*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
B: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
C: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
D: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
E: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
F: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6098
Polymers30,4996
Non-polymers1102
Water4,846269
1
A: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
B: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2213
Polymers10,1662
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-9 kcal/mol
Surface area5840 Å2
MethodPISA
2
C: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
D: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*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
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area5770 Å2
MethodPISA
3
E: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
F: DNA/RNA (5'-R(*AP*GP*AP*GP*AP*A)-D(P*G)-R(P*AP*UP*(RSP)P*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2213
Polymers10,1662
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area5830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.502, 42.502, 122.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 5083.128 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.06 M Manganese (II) chloride, 15.00 % w/v Polyethylene glycol 20,000

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 17, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.919→50 Å / Num. obs: 18877 / % possible obs: 99.3 % / Redundancy: 5 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rrim(I) all: 0.049 / Χ2: 0.863 / Net I/σ(I): 32.8
Reflection shellResolution: 1.919→1.95 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 919 / CC1/2: 0.859 / CC star: 0.961 / Rpim(I) all: 0.284 / Rrim(I) all: 0.638 / Χ2: 0.82 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.919→36.808 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.198 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.19
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2566 779 4.447 %
Rwork0.1873 16740 -
all0.19 --
obs-17519 92.361 %
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: 14.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å20 Å2
2---0.001 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.919→36.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2010 2 269 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0112244
X-RAY DIFFRACTIONr_bond_other_d0.0020.019936
X-RAY DIFFRACTIONr_angle_refined_deg2.0581.8973480
X-RAY DIFFRACTIONr_angle_other_deg0.5651.7282286
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.177560
X-RAY DIFFRACTIONr_chiral_restr0.0740.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined0.1060.2303
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21192
X-RAY DIFFRACTIONr_nbtor_refined0.2440.2821
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1220.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.237
X-RAY DIFFRACTIONr_nbd_other0.1670.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.219
X-RAY DIFFRACTIONr_scbond_it1.3511.7462244
X-RAY DIFFRACTIONr_scbond_other1.3511.7452245
X-RAY DIFFRACTIONr_scangle_it2.0463.1863480
X-RAY DIFFRACTIONr_scangle_other2.0463.1853481
X-RAY DIFFRACTIONr_lrange_it3.73524.033206
X-RAY DIFFRACTIONr_lrange_other3.49323.6793124
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
1.919-1.9690.354530.2496530.25713850.9160.96150.97470.226
1.969-2.0230.305280.2358380.23714040.9490.96561.68090.198
2.023-2.0810.286620.22411260.22713060.9510.96990.96480.19
2.081-2.1450.334760.24111980.24612770.9340.96299.76510.215
2.145-2.2150.301360.22912360.23112740.9370.96899.8430.205
2.215-2.2930.352340.23111560.23411910.9320.96799.9160.212
2.293-2.3790.241530.21511230.21711780.9610.97399.83020.192
2.379-2.4760.33600.21610550.22311180.9350.97599.73170.2
2.476-2.5850.324500.2119650.21610670.9390.97495.12650.198
2.585-2.7110.221430.1969730.19710220.9740.97699.41290.187
2.711-2.8560.294260.2049660.2079920.9360.9751000.203
2.856-3.0290.251480.1818900.1849390.9640.98299.89350.196
3.029-3.2360.219320.1698220.1718550.9740.98999.8830.193
3.236-3.4930.213440.1587820.168260.980.9911000.183
3.493-3.8230.172400.146990.1427410.9820.99199.73010.168
3.823-4.2690.164280.1226530.1236810.9860.9911000.146
4.269-4.9180.204300.1385210.1415860.9740.98994.02730.177
4.918-5.9970.13140.1375030.1375080.9990.99199.80310.171
5.997-8.370.226200.2223690.2233890.9790.9821000.288
8.37-36.8080.423120.2272120.2392250.9450.97399.55560.295

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