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- PDB-9yd3: RNA primer non-enzymatic extension product with RNA substrate -

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Basic information

Entry
Database: PDB / ID: 9yd3
TitleRNA primer non-enzymatic extension product with RNA substrate
ComponentsRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3')
KeywordsRNA / Nonenzymatic RNA primer extension / Product / RNA duplex / Origin of Life
Function / homologyChem-EQ4 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 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: To Be Published
Title: Nonenzymatic RNA copying with deoxypurine
Authors: Fang, Z. / Szostak, J.W.
History
DepositionSep 21, 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*GP*G)-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,79113
Polymers9,7162
Non-polymers1,07511
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.338, 47.338, 83.136
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-106-

MG

21B-105-

MG

31A-258-

HOH

41A-263-

HOH

51B-253-

HOH

61B-262-

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*GP*G)-3')


Mass: 4858.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-EQ4 / 5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]guanosine


Type: RNA linking / Mass: 428.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N8O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 298 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: 1.592→50 Å / Num. obs: 14954 / % possible obs: 99.3 % / Redundancy: 8.4 % / CC1/2: 0.982 / CC star: 0.995 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.022 / Rrim(I) all: 0.062 / Χ2: 0.902 / Net I/σ(I): 37.2
Reflection shellResolution: 1.592→1.63 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 650 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.139 / Rrim(I) all: 0.366 / Χ2: 0.981 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.592→41.568 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.814 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2474 682 5.467 %
Rwork0.2264 11793 -
all0.227 --
obs-12475 82.979 %
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: 16.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0.002 Å2-0 Å2
2---0.005 Å20 Å2
3---0.015 Å2
Refinement stepCycle: LAST / Resolution: 1.592→41.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 644 67 132 843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.016788
X-RAY DIFFRACTIONr_bond_other_d0.0240.023350
X-RAY DIFFRACTIONr_angle_refined_deg2.9682.2331208
X-RAY DIFFRACTIONr_angle_other_deg3.6422.365824
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.085516
X-RAY DIFFRACTIONr_chiral_restr0.4460.2156
X-RAY DIFFRACTIONr_chiral_restr_other1.9270.218
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021418
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023136
X-RAY DIFFRACTIONr_nbd_refined0.1020.279
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.2430
X-RAY DIFFRACTIONr_nbtor_refined0.2480.2316
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.2230.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2104
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.225
X-RAY DIFFRACTIONr_nbd_other0.1730.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.231
X-RAY DIFFRACTIONr_scbond_it2.7262.062788
X-RAY DIFFRACTIONr_scbond_other2.7252.07789
X-RAY DIFFRACTIONr_scangle_it4.3753.7521208
X-RAY DIFFRACTIONr_scangle_other4.3733.761209
X-RAY DIFFRACTIONr_lrange_it6.82523.0561162
X-RAY DIFFRACTIONr_lrange_other6.63822.5551109
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
1.592-1.6340.526170.2353940.24410980.8890.96937.43170.178
1.634-1.6780.351260.2444630.24910580.9690.96546.21930.196
1.678-1.7270.201210.2135020.21310170.980.97451.42580.17
1.727-1.780.28420.2565570.25810070.9520.95759.48360.208
1.78-1.8380.285500.2376430.249700.9350.96371.44330.209
1.838-1.9030.245340.2468080.2469510.950.95988.53840.215
1.903-1.9740.205510.2598560.2559120.9710.95799.45180.221
1.974-2.0550.314450.2618390.2638840.9370.9561000.231
2.055-2.1460.298520.2327830.2368350.9510.9651000.211
2.146-2.250.246540.2487630.2488170.9620.961000.236
2.25-2.3720.181450.2287230.2257680.9820.9681000.223
2.372-2.5150.292510.2376870.247390.940.96499.86470.246
2.515-2.6880.337420.2596390.2656810.9390.9551000.263
2.688-2.9020.371370.2446230.2516600.9380.9661000.276
2.902-3.1780.149260.2115820.2086130.9780.97899.18430.259
3.178-3.550.187340.1934980.1935330.9750.98299.81240.25
3.55-4.0950.164200.1724760.1714960.9920.9851000.231
4.095-5.0030.151170.1614100.164270.990.9841000.222
5.003-7.0240.271100.2093340.2113440.9650.9781000.345
7.024-41.5680.50280.3542130.3572210.5660.9221000.439

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