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- PDB-9lke: Crystal structure of Guanine-II riboswitch in complex with hypoxa... -

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Basic information

Entry
Database: PDB / ID: 9lke
TitleCrystal structure of Guanine-II riboswitch in complex with hypoxanthine
ComponentsPRTg (70-MER)
KeywordsRNA / guanine-II riboswitch / hypoxanthine
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / HYPOXANTHINE / RNA / RNA (> 10)
Function and homology information
Biological speciesPaenibacillus sp. FSL E2-0178 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsLi, H.C. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Ligand specificity and adaptability revealed by the first Guanine-II riboswitch tertiary structure.
Authors: Li, H. / Shen, X. / Xu, X. / Tai, X. / He, M. / Zhang, J. / Ren, A.
History
DepositionJan 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRTg (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1906
Polymers22,4571
Non-polymers7325
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.927, 50.615, 218.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain PRTg (70-MER)


Mass: 22457.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FSL E2-0178 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.27 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.10202 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10202 Å / Relative weight: 1
ReflectionResolution: 2.26→36.44 Å / Num. obs: 10274 / % possible obs: 99.8 % / Redundancy: 11.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Net I/σ(I): 17.5
Reflection shellResolution: 2.26→2.4 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3 / Num. unique obs: 1630 / CC1/2: 0.95 / Rpim(I) all: 0.287 / Rrim(I) all: 0.739

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→30.35 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1015 9.98 %
Rwork0.228 --
obs0.2303 10169 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→30.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1520 13 13 1546
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051708
X-RAY DIFFRACTIONf_angle_d1.0612657
X-RAY DIFFRACTIONf_dihedral_angle_d19.48851
X-RAY DIFFRACTIONf_chiral_restr0.048354
X-RAY DIFFRACTIONf_plane_restr0.00772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.380.47461440.3681291X-RAY DIFFRACTION100
2.38-2.530.41381410.36871278X-RAY DIFFRACTION100
2.53-2.730.44451430.39251282X-RAY DIFFRACTION100
2.73-30.40251400.34961287X-RAY DIFFRACTION99
3-3.440.28361450.25551297X-RAY DIFFRACTION98
3.44-4.330.22471460.20561319X-RAY DIFFRACTION99
4.33-30.350.17821560.16611400X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -6.885 Å / Origin y: -8.388 Å / Origin z: -26.2056 Å
111213212223313233
T0.6483 Å20.088 Å2-0.0885 Å2-0.4685 Å2-0.0026 Å2--0.6243 Å2
L2.4848 °20.4518 °20.8428 °2-0.264 °20.459 °2--2.8501 °2
S-0.1401 Å °0.4516 Å °0.0029 Å °-0.1829 Å °0.0341 Å °0.1438 Å °-0.441 Å °-0.0235 Å °0.1343 Å °
Refinement TLS groupSelection details: all

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