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- PDB-9okw: 16mer self-complementary duplex RNA with dG:C pair sequence 1 -

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Basic information

Entry
Database: PDB / ID: 9okw
Title16mer self-complementary duplex RNA with dG:C pair sequence 1
ComponentsDNA/RNA (5'-R(*A)-D(P*G)-R(P*AP*GP*AP*AP*GP*AP*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: 1.54 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(*A)-D(P*G)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1163
Polymers5,0671
Non-polymers492
Water1,65792
1
A: DNA/RNA (5'-R(*A)-D(P*G)-R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,2316
Polymers10,1342
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1710 Å2
ΔGint-21 kcal/mol
Surface area5970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.258, 41.258, 124.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-222-

HOH

21A-229-

HOH

31A-250-

HOH

41A-265-

HOH

51A-274-

HOH

61A-275-

HOH

71A-285-

HOH

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Components

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


Mass: 5067.063 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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25 % v/v Polyethylene glycol monomethyl ether 550, 50 mM HEPES pH 7.0, 10 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 6327 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 10 Å2 / CC1/2: 0.974 / CC star: 0.993 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.032 / Rrim(I) all: 0.093 / Χ2: 0.947 / Net I/σ(I): 24.5
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 294 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.169 / Rrim(I) all: 0.373 / Χ2: 0.885 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→41.53 Å / SU ML: 0.117 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7992
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 569 9.98 %
Rwork0.1986 5131 -
obs0.2036 5700 90.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.82 Å2
Refinement stepCycle: LAST / Resolution: 1.54→41.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 335 2 92 429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022374
X-RAY DIFFRACTIONf_angle_d0.4842580
X-RAY DIFFRACTIONf_chiral_restr0.022378
X-RAY DIFFRACTIONf_plane_restr0.003116
X-RAY DIFFRACTIONf_dihedral_angle_d5.9447186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.70.3034950.2354855X-RAY DIFFRACTION61.77
1.7-1.940.28011520.22041381X-RAY DIFFRACTION99.1
1.94-2.450.29651580.23151411X-RAY DIFFRACTION99.68
2.45-41.530.20271640.16871484X-RAY DIFFRACTION99.04

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