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- PDB-9ol0: 16mer self-complementary duplex RNA with dI:s(2)C pair sequence 1 -

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Basic information

Entry
Database: PDB / ID: 9ol0
Title16mer self-complementary duplex RNA with dI:s(2)C pair sequence 1
ComponentsDNA/RNA (5'-R(*A)-D(P*I)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*(RSP)P*U)-3')
KeywordsRNA / Deoxyribo-purine / deoxyinosine / 2-thiocytidine / 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: 1.15 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,1414
Polymers5,0681
Non-polymers733
Water1,38777
1
A: DNA/RNA (5'-R(*A)-D(P*I)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*(RSP)P*U)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,2828
Polymers10,1362
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area1810 Å2
ΔGint-29 kcal/mol
Surface area6070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.293, 41.293, 124.404
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11A-212-

HOH

21A-243-

HOH

31A-253-

HOH

41A-267-

HOH

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Components

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


Mass: 5068.114 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.: 77 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.15→34.37 Å / Num. obs: 14617 / % possible obs: 98.1 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.029 / Rrim(I) all: 0.068 / Net I/σ(I): 14.9
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.256 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 819 / CC1/2: 0.431 / Rpim(I) all: 0.677 / Rrim(I) all: 1.434 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→34.37 Å / SU ML: 0.1658 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 27.2785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 1461 10.01 %
Rwork0.2026 13133 -
obs0.2057 14594 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.02 Å2
Refinement stepCycle: LAST / Resolution: 1.15→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 3 77 414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128373
X-RAY DIFFRACTIONf_angle_d1.7726578
X-RAY DIFFRACTIONf_chiral_restr0.059876
X-RAY DIFFRACTIONf_plane_restr0.019316
X-RAY DIFFRACTIONf_dihedral_angle_d7.427173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.190.35941390.32211260X-RAY DIFFRACTION94.98
1.19-1.240.29151410.27991260X-RAY DIFFRACTION96.62
1.24-1.30.29621430.26981284X-RAY DIFFRACTION97.27
1.3-1.370.30761440.26971294X-RAY DIFFRACTION97.69
1.37-1.450.29991440.2531302X-RAY DIFFRACTION98.03
1.45-1.560.2351460.2341305X-RAY DIFFRACTION98.44
1.56-1.720.25111470.2171322X-RAY DIFFRACTION98.52
1.72-1.970.23251480.20271331X-RAY DIFFRACTION99.13
1.97-2.480.24711490.22031344X-RAY DIFFRACTION99.53
2.48-34.370.20251600.1681431X-RAY DIFFRACTION99.19

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