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- PDB-9lku: Crystal structure of the 2'-dG-III riboswitch bound to Guanosine -

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Basic information

Entry
Database: PDB / ID: 9lku
TitleCrystal structure of the 2'-dG-III riboswitch bound to Guanosine
ComponentsRNA (65-MER)
KeywordsRNA / Riboswitch / 2'-dG / Guanosine
Function / homologyGUANOSINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsShen, X. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structure-based insights into the ligand specificity tuning of 2'-dG-III riboswitch.
Authors: Shen, X. / Li, H. / Xu, X. / Song, Q. / Tai, X. / He, M. / Ren, A.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: RNA (65-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2704
Polymers20,9381
Non-polymers3323
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-5 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.323, 70.906, 116.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain RNA (65-MER)


Mass: 20938.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.39 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.012 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M sodium cacodylate trihydrate 7.0, 35 % v/v 2-Methyl-2,4-pentanediol, 0.012 M spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.74→58.13 Å / Num. obs: 5513 / % possible obs: 99.7 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.028 / Rrim(I) all: 0.095 / Χ2: 0.97 / Net I/σ(I): 17.8
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.655 / Num. unique obs: 793 / CC1/2: 0.961 / Rpim(I) all: 0.205 / Rrim(I) all: 0.687 / Χ2: 0.94

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→39.93 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 540 10.05 %
Rwork0.2009 --
obs0.2078 5375 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1406 2 2 1410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051570
X-RAY DIFFRACTIONf_angle_d1.2462441
X-RAY DIFFRACTIONf_dihedral_angle_d17.997780
X-RAY DIFFRACTIONf_chiral_restr0.055327
X-RAY DIFFRACTIONf_plane_restr0.00766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-3.010.36571350.27911199X-RAY DIFFRACTION98
3.01-3.450.33211270.27081147X-RAY DIFFRACTION93
3.45-4.350.28561350.20081194X-RAY DIFFRACTION98
4.35-39.930.20181430.15741295X-RAY DIFFRACTION99

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