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

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Basic information

Entry
Database: PDB / ID: 9lkv
TitleCrystal structure of the 2'-dG-III riboswitch bound to 2'-dG
ComponentsRNA (73-MER)
KeywordsRNA / Riboswitch / 2'-dG
Function / homology2'-DEOXY-GUANOSINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 (73-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7713
Polymers23,4801
Non-polymers2922
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-3 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.415, 44.993, 51.508
Angle α, β, γ (deg.)90.00, 116.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (73-MER)


Mass: 23479.760 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-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.23 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.04 M sodium cacodylate trihydrate 7.0, 30 % v/v 2-Methyl-2,4-pentanediol, 0.012 M spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.13→43.16 Å / Num. obs: 11392 / % possible obs: 97.4 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Χ2: 0.9 / Net I/σ(I): 14.2 / Num. measured all: 76012
Reflection shellResolution: 2.13→2.24 Å / % possible obs: 96.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.954 / Num. measured all: 10962 / Num. unique obs: 1654 / CC1/2: 0.883 / Rpim(I) all: 0.4 / Rrim(I) all: 1.036 / Χ2: 0.81 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→43.16 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2649 1135 10.09 %
Rwork0.231 --
obs0.2346 11252 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→43.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1573 1 7 1581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051757
X-RAY DIFFRACTIONf_angle_d1.1392731
X-RAY DIFFRACTIONf_dihedral_angle_d16.56876
X-RAY DIFFRACTIONf_chiral_restr0.046366
X-RAY DIFFRACTIONf_plane_restr0.00774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.230.40661370.4111264X-RAY DIFFRACTION96
2.23-2.340.39771350.36291258X-RAY DIFFRACTION96
2.34-2.490.36711460.34441249X-RAY DIFFRACTION96
2.49-2.680.48861310.34591258X-RAY DIFFRACTION96
2.68-2.950.35421490.31411262X-RAY DIFFRACTION96
2.95-3.380.33021420.29131231X-RAY DIFFRACTION93
3.38-4.260.23551410.21631276X-RAY DIFFRACTION96
4.26-43.160.19511540.15831319X-RAY DIFFRACTION97

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