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- PDB-9ol3: DNA-imidazolium-bridged dinucleotide intermediate complex -

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Basic information

Entry
Database: PDB / ID: 9ol3
TitleDNA-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 / deoxyribo-purine / Origin of Life
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.557 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: 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)10,52111
Polymers8,8662
Non-polymers1,6559
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-29 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.241, 48.241, 82.663
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-254-

HOH

21A-259-

HOH

31B-252-

HOH

41B-256-

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-A1CGJ / 2-amino-1-[(R)-{[(2R,3S,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-3-[(S)-{[(2R,3S,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]-1H-imidazol-3-ium (non-preferred name)


Mass: 742.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H30N13O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M HEPES pH 7.0, 0.2 M Ammonium acetate, 0.15 M Magnesium acetate, 10% w/v Polyethylene glycol 6,000.

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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: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033175 Å / Relative weight: 1
ReflectionResolution: 1.557→50 Å / Num. obs: 15265 / % possible obs: 92.4 % / Redundancy: 6.5 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Χ2: 1.236 / Net I/σ(I): 49.6
Reflection shellResolution: 1.557→1.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 433 / CC1/2: 0.965 / CC star: 0.991 / Rpim(I) all: 0.231 / Rrim(I) all: 0.498 / Χ2: 0.569 / % possible all: 55.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.557→41.778 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.633 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2494 768 5.031 %
Rwork0.2039 14497 -
all0.206 --
obs-15265 92.291 %
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: 48.136 Å2
Baniso -1Baniso -2Baniso -3
1--0.007 Å2-0.003 Å2-0 Å2
2---0.007 Å20 Å2
3---0.022 Å2
Refinement stepCycle: LAST / Resolution: 1.557→41.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 598 107 130 835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.017784
X-RAY DIFFRACTIONr_bond_other_d0.0260.023354
X-RAY DIFFRACTIONr_angle_refined_deg2.9332.3231202
X-RAY DIFFRACTIONr_angle_other_deg3.4762.482832
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.051514
X-RAY DIFFRACTIONr_chiral_restr0.1760.2152
X-RAY DIFFRACTIONr_chiral_restr_other1.5520.224
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023136
X-RAY DIFFRACTIONr_nbd_refined0.090.259
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.2431
X-RAY DIFFRACTIONr_nbtor_refined0.2530.2311
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2370.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2114
X-RAY DIFFRACTIONr_metal_ion_refined0.1140.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.29
X-RAY DIFFRACTIONr_nbd_other0.1750.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.221
X-RAY DIFFRACTIONr_scbond_it5.1195.91784
X-RAY DIFFRACTIONr_scbond_other5.1165.909785
X-RAY DIFFRACTIONr_scangle_it6.9810.7351202
X-RAY DIFFRACTIONr_scangle_other6.97810.7331203
X-RAY DIFFRACTIONr_lrange_it8.02972.9631165
X-RAY DIFFRACTIONr_lrange_other7.57772.2361100
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
1.557-1.5980.494280.4746240.47511890.6580.77154.8360.341
1.598-1.6410.399510.467510.45611590.8160.78669.19760.299
1.641-1.6890.494500.4929460.49211450.7010.75686.98690.338
1.689-1.7410.457390.40610170.40811120.7790.83194.9640.275
1.741-1.7980.478550.3449960.35110600.8580.89999.15090.28
1.798-1.8610.419570.2999780.30510470.9020.9398.85390.245
1.861-1.9310.381530.2689620.27310220.8920.94999.31510.237
1.931-2.010.379370.2689100.2729520.9270.94999.47480.233
2.01-2.0990.276330.2348920.2369360.9550.96498.82480.198
2.099-2.2010.279460.2158270.2198920.9530.9797.870.188
2.201-2.320.375620.2057840.2158530.9580.97299.17940.191
2.32-2.460.295460.1967420.2028060.9520.97597.76680.184
2.46-2.6290.256410.2216940.2237550.9640.96897.3510.215
2.629-2.8390.262470.2266650.2287240.9560.96798.34250.231
2.839-3.1080.248210.2186230.2196600.9460.97397.57580.233
3.108-3.4730.227210.25690.2016050.9730.9897.52070.237
3.473-4.0050.229250.1755130.1785460.9810.98698.53480.221
4.005-4.8940.23240.1484310.1514650.9580.98697.84950.205
4.894-6.8750.178270.1763460.1763750.9840.98399.46670.256
6.875-41.7780.45750.2742270.2792340.9250.94499.14530.331

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