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- PDB-36lm: RNA-dGMP complex -

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Basic information

Entry
Database: PDB / ID: 36lm
TitleRNA-dGMP complex
ComponentsRNA (16-mer)
KeywordsRNA / Nonenzymatic RNA replication / Chirality
Function / homologyACETATE ION / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsEssex, J. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)2325198 United States
CitationJournal: To Be Published
Title: Effects of Chemically Activated L-Nucleotides on Nonenzymatic RNA Copying
Authors: Essex, J. / Jia, X. / Zhang, J. / Szostak, J.W.
History
DepositionJun 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: 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 (16-mer)
B: RNA (16-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,65413
Polymers9,0262
Non-polymers1,62811
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-19 kcal/mol
Surface area7100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.819, 49.819, 81.324
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
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

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Components

#1: RNA chain RNA (16-mer)


Mass: 4512.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% w/v Polyethylene glycol 6,000, 50 mM HEPES pH 7.0, 200 mM Ammonium acetate, 150 mM Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2025
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.42→19.06 Å / Num. obs: 14931 / % possible obs: 88.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.59 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.4
Reflection shellResolution: 1.42→1.62 Å / Num. unique obs: 747 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→19.06 Å / SU ML: 0.1538 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2387 1484 9.94 %
Rwork0.2227 13440 -
obs0.2243 14924 65.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.09 Å2
Refinement stepCycle: LAST / Resolution: 1.42→19.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 598 105 85 788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007778
X-RAY DIFFRACTIONf_angle_d1.20481218
X-RAY DIFFRACTIONf_chiral_restr0.0375144
X-RAY DIFFRACTIONf_plane_restr0.004734
X-RAY DIFFRACTIONf_dihedral_angle_d19.887396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.460.648740.267726X-RAY DIFFRACTION1.5
1.47-1.520.4338120.3004110X-RAY DIFFRACTION6.07
1.52-1.580.2203280.3123217X-RAY DIFFRACTION12.45
1.58-1.650.3095700.2412660X-RAY DIFFRACTION35.87
1.65-1.740.28441610.24061463X-RAY DIFFRACTION79.37
1.74-1.850.24151920.21651754X-RAY DIFFRACTION95.67
1.85-1.990.23911940.22441785X-RAY DIFFRACTION96.11
1.99-2.190.26931940.23211795X-RAY DIFFRACTION96.84
2.19-2.50.23682050.25151811X-RAY DIFFRACTION97.34
2.5-3.150.2912040.2561858X-RAY DIFFRACTION97.68
3.15-19.060.19792200.18581961X-RAY DIFFRACTION98.33

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