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- PDB-9ljn: Crystal structure of Guanine-II riboswitch in complex with guanine -

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Basic information

Entry
Database: PDB / ID: 9ljn
TitleCrystal structure of Guanine-II riboswitch in complex with guanine
ComponentsPRTg (71-MER)
KeywordsRNA / riboswitch / guanine
Function / homologyGUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciesPaenibacillus sp. FSL E2-0178 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 15, 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

Downloads & links

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Assembly

Deposited unit
A: PRTg (71-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9783
Polymers22,8031
Non-polymers1752
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.024, 49.112, 120.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222

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Components

#1: RNA chain PRTg (71-MER)


Mass: 22802.533 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-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O / 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.: 19 / 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: 2.43 Å3/Da / Density % sol: 50.07 %
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: 2.75→60.16 Å / Num. obs: 6256 / % possible obs: 99.1 % / Redundancy: 12.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Net I/σ(I): 17.4
Reflection shellResolution: 2.75→2.89 Å / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 896 / CC1/2: 0.981 / Rpim(I) all: 0.331 / Rrim(I) all: 0.867

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
PDB_EXTRACTdata extraction
PHENIX1.20.1_4487phasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→31.06 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 606 10.04 %
Rwork0.217 --
obs0.2207 6036 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1511 12 19 1542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051701
X-RAY DIFFRACTIONf_angle_d1.1462646
X-RAY DIFFRACTIONf_dihedral_angle_d20.336859
X-RAY DIFFRACTIONf_chiral_restr0.052355
X-RAY DIFFRACTIONf_plane_restr0.00672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-3.020.45151440.43521318X-RAY DIFFRACTION95
3.02-3.460.38231470.33531291X-RAY DIFFRACTION92
3.46-4.360.3071490.22331325X-RAY DIFFRACTION95
4.36-31.060.1831660.16591496X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.0079 Å / Origin y: 11.3749 Å / Origin z: 28.8248 Å
111213212223313233
T1.4843 Å2-0.0383 Å2-0.1537 Å2-1.0353 Å20.0586 Å2--0.5184 Å2
L4.8314 °2-0.6233 °2-0.9145 °2-2.157 °20.3745 °2--0.133 °2
S-0.4237 Å °-0.7749 Å °0.1194 Å °0.9702 Å °0.3826 Å °-0.2043 Å °-0.886 Å °0.2035 Å °0.082 Å °
Refinement TLS groupSelection details: all

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