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- PDB-9iwf: crystal structure of P. beijingensis xanthine-II riboswitch in co... -

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Basic information

Entry
Database: PDB / ID: 9iwf
Titlecrystal structure of P. beijingensis xanthine-II riboswitch in complex with xanthine
ComponentsP. beijingensis xanthine-II riboswitch (70-MER)
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: 2.06 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: P. beijingensis xanthine-II riboswitch (70-MER)
B: P. beijingensis xanthine-II riboswitch (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,84121
Polymers44,1262
Non-polymers1,71519
Water1,982110
1
A: P. beijingensis xanthine-II riboswitch (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,93311
Polymers22,0631
Non-polymers87010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P. beijingensis xanthine-II riboswitch (70-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,90910
Polymers22,0631
Non-polymers8459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.585, 115.752, 126.759
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 P. beijingensis xanthine-II riboswitch (70-MER)


Mass: 22063.092 Da / Num. of mol.: 2 / 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.: 15 / 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.: 110 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Magnesium chloride, 0.04 M Sodium cacodylate pH 5.5, 40% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.002 M Hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.06→85.48 Å / Num. obs: 24728 / % possible obs: 97.2 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Χ2: 0.92 / Net I/σ(I): 19.5 / Num. measured all: 307642
Reflection shellResolution: 2.06→2.17 Å / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 1.198 / Num. measured all: 46330 / Num. unique obs: 3588 / CC1/2: 0.793 / Rpim(I) all: 0.344 / Rrim(I) all: 1.247 / Χ2: 0.83 / Net I/σ(I) obs: 2.4

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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: 2.06→30.56 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1999 8.11 %
Rwork0.2187 --
obs0.2215 24648 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→30.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2986 37 110 3133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053354
X-RAY DIFFRACTIONf_angle_d1.1315216
X-RAY DIFFRACTIONf_dihedral_angle_d16.3581698
X-RAY DIFFRACTIONf_chiral_restr0.051698
X-RAY DIFFRACTIONf_plane_restr0.007144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.37641390.3321576X-RAY DIFFRACTION100
2.11-2.160.35611450.3061642X-RAY DIFFRACTION100
2.16-2.230.38771460.29791656X-RAY DIFFRACTION100
2.23-2.30.34311100.2881248X-RAY DIFFRACTION78
2.3-2.380.34161460.29171657X-RAY DIFFRACTION100
2.38-2.480.30231440.2941633X-RAY DIFFRACTION100
2.48-2.590.311480.30651661X-RAY DIFFRACTION100
2.59-2.730.41511430.31361629X-RAY DIFFRACTION100
2.73-2.90.38291470.30631680X-RAY DIFFRACTION100
2.9-3.120.30051460.26161641X-RAY DIFFRACTION100
3.12-3.430.2371480.21011677X-RAY DIFFRACTION100
3.43-3.930.24781240.18831413X-RAY DIFFRACTION83
3.93-4.950.18711520.1631710X-RAY DIFFRACTION100
4.95-30.560.17991610.1691826X-RAY DIFFRACTION99

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