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- PDB-9iwg: crystal structure of xanthine-II ML2/3 in complex with xanthine -

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Basic information

Entry
Database: PDB / ID: 9iwg
Titlecrystal structure of xanthine-II ML2/3 in complex with xanthine
Componentsxanthine-II ML2/3
KeywordsRNA / riboswitch / xanthine
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / XANTHINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesPaenibacillus beijingensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsXu, X.C. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci China Life Sci / Year: 2025
Title: Structure-based principles underlying ligand recognition of xanthine-II riboswitch.
Authors: Xu, X. / He, M. / Tai, X. / Ren, Q. / Shen, X. / Li, C. / Ren, A.
History
DepositionJul 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: xanthine-II ML2/3
B: xanthine-II ML2/3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,18830
Polymers44,2542
Non-polymers1,93428
Water1,53185
1
A: xanthine-II ML2/3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,09415
Polymers22,1271
Non-polymers96714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: xanthine-II ML2/3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,09415
Polymers22,1271
Non-polymers96714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.348, 117.816, 125.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain xanthine-II ML2/3


Mass: 22127.139 Da / Num. of mol.: 2 / Mutation: C22U, U26G, C49A / Source method: obtained synthetically / Source: (synth.) Paenibacillus beijingensis (bacteria) / References: GenBank: 779742186
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.04 M Lithium chloride, 0.08 M Strontium chlorid, 0.02 M Magnesium chloride, 0.04 M Sodium cacodylate pH 7.0, 30% 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: 1.009 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.48→62.81 Å / Num. obs: 14497 / % possible obs: 97.8 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.025 / Rrim(I) all: 0.086 / Χ2: 0.99 / Net I/σ(I): 22.3 / Num. measured all: 177516
Reflection shellResolution: 2.48→2.61 Å / % possible obs: 99.9 % / Redundancy: 13 % / Rmerge(I) obs: 0.976 / Num. measured all: 27618 / Num. unique obs: 2119 / CC1/2: 0.829 / Rpim(I) all: 0.278 / Rrim(I) all: 1.015 / Χ2: 0.87 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→42.97 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 1446 10.02 %
Rwork0.2328 --
obs0.2364 14424 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2996 46 85 3127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023368
X-RAY DIFFRACTIONf_angle_d0.5765240
X-RAY DIFFRACTIONf_dihedral_angle_d15.3911698
X-RAY DIFFRACTIONf_chiral_restr0.028698
X-RAY DIFFRACTIONf_plane_restr0.002144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.570.41031520.35771278X-RAY DIFFRACTION100
2.57-2.650.35241150.34281136X-RAY DIFFRACTION99
2.68-2.790.36871300.31471190X-RAY DIFFRACTION100
2.79-2.940.32541480.31031327X-RAY DIFFRACTION100
2.94-3.120.35131440.29071267X-RAY DIFFRACTION100
3.12-3.360.30361480.2421329X-RAY DIFFRACTION99
3.36-3.70.2671490.2251312X-RAY DIFFRACTION100
3.7-4.240.23841440.18321331X-RAY DIFFRACTION100
4.24-5.330.20991530.19361372X-RAY DIFFRACTION100
5.34-42.970.2271630.21511436X-RAY DIFFRACTION99

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