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- PDB-9ol2: RNA-imidazolium-bridged dinucleotide intermediate complex -

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Basic information

Entry
Database: PDB / ID: 9ol2
TitleRNA-imidazolium-bridged dinucleotide intermediate complex
ComponentsRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
KeywordsRNA / Imidazolium-bridged dinucleotide / RNA duplex / Origin of Life
Function / homologyChem-EQ1 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.528 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: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,58511
Polymers8,8662
Non-polymers1,7199
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.592, 49.592, 81.941
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-275-

HOH

21A-286-

HOH

31A-297-

HOH

41B-275-

HOH

51B-285-

HOH

61B-298-

HOH

71B-299-

HOH

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Components

#1: RNA chain RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')


Mass: 4432.824 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-EQ1 / 2-amino-1-[(R)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-3-[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium


Mass: 774.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30N13O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% w/v Polyethylene glycol 6,000, 0.05 M HEPES pH 7.0, 0.2 M Ammonium acetate, 0.15 M Magnesium acetate

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033175 Å / Relative weight: 1
ReflectionResolution: 1.528→50 Å / Num. obs: 17783 / % possible obs: 96.9 % / Redundancy: 5.9 % / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.035 / Rrim(I) all: 0.087 / Χ2: 0.939 / Net I/σ(I): 15.9
Reflection shellResolution: 1.528→1.56 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 757 / CC1/2: 0.86 / CC star: 0.962 / Rpim(I) all: 0.203 / Rrim(I) all: 0.464 / Χ2: 0.678 / % possible all: 84.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.528→42.948 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.389 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2345 889 5.037 %
Rwork0.1984 16762 -
all0.2 --
obs-17651 96.448 %
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: 15.946 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.528→42.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 598 111 201 910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.017788
X-RAY DIFFRACTIONr_bond_other_d0.0270.023350
X-RAY DIFFRACTIONr_angle_refined_deg3.0412.3261210
X-RAY DIFFRACTIONr_angle_other_deg3.6072.48824
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.089514
X-RAY DIFFRACTIONr_chiral_restr0.480.2156
X-RAY DIFFRACTIONr_chiral_restr_other1.820.220
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023136
X-RAY DIFFRACTIONr_nbd_refined0.0750.257
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.2465
X-RAY DIFFRACTIONr_nbtor_refined0.2440.2310
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2460.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2156
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0790.210
X-RAY DIFFRACTIONr_nbd_other0.1530.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.264
X-RAY DIFFRACTIONr_scbond_it2.2771.977788
X-RAY DIFFRACTIONr_scbond_other2.2761.977789
X-RAY DIFFRACTIONr_scangle_it3.493.6221210
X-RAY DIFFRACTIONr_scangle_other3.4883.6221211
X-RAY DIFFRACTIONr_lrange_it5.84625.3531199
X-RAY DIFFRACTIONr_lrange_other5.12524.2111126
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
1.528-1.5670.299730.26311520.26513260.9620.96292.38310.243
1.567-1.610.326710.23512150.23912970.9290.96799.15190.212
1.61-1.6570.229610.21311840.21312620.9720.97198.65290.196
1.657-1.7080.201530.19811520.19812190.9770.97698.85150.189
1.708-1.7640.203730.18710910.18811830.9730.97798.39390.181
1.764-1.8260.247610.19510840.19811530.9620.97599.30620.193
1.826-1.8940.319650.20210180.20811080.9440.97497.74370.204
1.894-1.9720.275560.19910060.20210710.9540.97599.15970.203
1.972-2.0590.213510.1989700.19910270.9730.97599.41580.204
2.059-2.1590.248390.2089470.2110000.970.97498.60.227
2.159-2.2760.209500.1878730.1899430.9770.97797.87910.204
2.276-2.4130.259300.1688410.1718860.9480.98298.3070.193
2.413-2.5790.302290.188150.1848540.960.97898.8290.213
2.579-2.7850.215260.1937420.1947810.9690.97798.33550.236
2.785-3.050.205470.1966570.1977350.970.97695.78230.247
3.05-3.4080.218390.25680.2016630.9690.97791.55350.258
3.408-3.9310.27160.2015020.2035960.9390.97586.91280.256
3.931-4.8040.257270.1764100.185210.9640.98383.87720.236
4.804-6.7520.14190.1883400.1864110.9860.98187.34790.28
6.752-42.9480.11130.3291950.3242640.9680.926750.429

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