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- PDB-36lc: RNA-L-G monomer complex -

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Basic information

Entry
Database: PDB / ID: 36lc
TitleRNA-L-G monomer complex
ComponentsRNA (16-mer)
KeywordsRNA / Nonenzymatic RNA replication / Chirality
Function / homologyL-GUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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: Effect 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)10,4786
Polymers9,0262
Non-polymers1,4534
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint9 kcal/mol
Surface area5970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.070, 48.070, 83.745
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-0G / L-GUANOSINE-5'-MONOPHOSPHATE


Type: L-RNA linking / Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.09 Å3/Da / Density % sol: 54.51 %
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: Jun 27, 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: 2.18→41.87 Å / Num. obs: 3092 / % possible obs: 88.2 % / Redundancy: 17.5 % / Biso Wilson estimate: 32.9 Å2 / CC1/2: 0.93 / Net I/σ(I): 5.9
Reflection shellResolution: 2.18→2.52 Å / Num. unique obs: 206 / CC1/2: 0.73

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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: 2.18→41.87 Å / SU ML: 0.2558 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3069 298 9.7 %
Rwork0.2721 2775 -
obs0.2755 3073 88.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.15 Å2
Refinement stepCycle: LAST / Resolution: 2.18→41.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 598 96 6 700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003776
X-RAY DIFFRACTIONf_angle_d1.02521220
X-RAY DIFFRACTIONf_chiral_restr0.0329148
X-RAY DIFFRACTIONf_plane_restr0.002232
X-RAY DIFFRACTIONf_dihedral_angle_d19.5446396
LS refinement shellResolution: 2.18→2.25 Å
RfactorNum. reflection% reflection
Rfree0.5406 45 -
Rwork0.4565 412 -
obs--65.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.30769918906-0.04089690733230.475748584640.4325112474940.701938345991.44065132294-0.295151439518-0.757457192817-0.8655155590350.6300362360360.523283370763-0.2949714023561.67296083334-0.186998702612-0.1032791602970.506007897677-0.09737164396590.0837160689526-0.1372409867820.2688660908330.471704810969-0.26203719894214.257043707225.9664218319
20.4694540845350.433873520681-0.07176122165110.3900984096460.1049072319121.06239782118-0.285261474550.086339503773-1.30706211064-0.6496996156890.1799656319630.1581644819371.479498583250.744356823081-0.1965939483960.710973689475-0.06794991727370.01832330979660.0249616806928-0.1776779216720.4475088131610.29779395509814.289112257815.9187931028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 14 )AA5 - 14
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 14 )BD5 - 14

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