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- PDB-9uw0: Crystal structure of 2'-dG-III riboswitch with Guanosine, mangane... -

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Basic information

Entry
Database: PDB / ID: 9uw0
TitleCrystal structure of 2'-dG-III riboswitch with Guanosine, manganese saok
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: 1.97 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
DepositionMay 11, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,6559
Polymers21,0181
Non-polymers6378
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.206, 70.365, 116.266
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: 21018.254 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.32 Å3/Da / Density % sol: 46.45 %
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: BL02U1 / Wavelength: 1.23984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23984 Å / Relative weight: 1
ReflectionResolution: 1.97→58.13 Å / Num. obs: 25859 / % possible obs: 97.6 % / Redundancy: 7.1 % / CC1/2: 0.999 / Net I/σ(I): 17
Reflection shellResolution: 1.97→2.07 Å / Num. unique obs: 2020 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→32.5 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2229 1303 5.04 %
Rwork0.2054 --
obs0.2063 25859 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1390 27 46 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051574
X-RAY DIFFRACTIONf_angle_d1.0742448
X-RAY DIFFRACTIONf_dihedral_angle_d15.568792
X-RAY DIFFRACTIONf_chiral_restr0.044329
X-RAY DIFFRACTIONf_plane_restr0.00867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.040.31411670.30252777X-RAY DIFFRACTION99
2.04-2.140.39431330.332753X-RAY DIFFRACTION97
2.14-2.240.3021450.28172587X-RAY DIFFRACTION98
2.27-2.390.29861000.26852521X-RAY DIFFRACTION100
2.39-2.570.29661640.272773X-RAY DIFFRACTION100
2.58-2.830.26291470.27242783X-RAY DIFFRACTION100
2.83-3.240.27991620.2172802X-RAY DIFFRACTION99
3.24-4.080.15941310.17792785X-RAY DIFFRACTION99
4.09-32.50.16891540.14722775X-RAY DIFFRACTION99

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