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- PDB-8q6n: Xanthin riboswitch in complex with oxypurinol -

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Basic information

Entry
Database: PDB / ID: 8q6n
TitleXanthin riboswitch in complex with oxypurinol
ComponentsXanthin riboswitch NMT-46 (46-MER)
KeywordsRNA / RNA riboswitch xanthin ligand
Function / homologyOxypurinol / RNA / RNA (> 10)
Function and homology information
Biological speciesIdeonella sp. B508-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsNar, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Engineering oxypurinol-responsive riboswitches based on bacterial xanthine aptamers for gene expression control in mammalian cell culture.
Authors: Hedwig, V. / Sporing, M. / Ottlinger, J. / Kose, S. / Nar, H. / Schnapp, G. / Gottschling, D. / Klein, H. / Aspnes, G. / Klugmann, M. / Hartig, J.S.
History
DepositionAug 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_database_related / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_related.content_type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xanthin riboswitch NMT-46 (46-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0562
Polymers14,9041
Non-polymers1521
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.811, 85.091, 97.162
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

#1: RNA chain Xanthin riboswitch NMT-46 (46-MER)


Mass: 14903.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oxypurinol / Source: (synth.) Ideonella sp. B508-1 (bacteria)
#2: Chemical ChemComp-141 / Oxypurinol / Alloxanthine


Mass: 152.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 5.05 Å3/Da / Density % sol: 75.64 %
Crystal growTemperature: 287 K / Method: vapor diffusion / pH: 7
Details: 0.1M ammonium sulfate, 0.1M sodium chloride, 20% PEG 8000, 1M sodium formate, 50mM Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.102 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 6639 / % possible obs: 98 % / Redundancy: 12 % / Biso Wilson estimate: 97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.013 / Net I/av σ(I): 23.3 / Net I/σ(I): 4.2
Reflection shellResolution: 2.66→2.76 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 332 / Rpim(I) all: 2.9 / % possible all: 84.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ELP

7elp


Resolution: 2.63→21.34 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.429 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.504 / SU Rfree Blow DPI: 0.336 / SU Rfree Cruickshank DPI: 0.317
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 318 -RANDOM
Rwork0.2371 ---
obs0.2391 6620 71.5 %-
Displacement parametersBiso mean: 123.43 Å2
Baniso -1Baniso -2Baniso -3
1-7.4481 Å20 Å20 Å2
2--0.3076 Å20 Å2
3----7.7557 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.63→21.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 987 11 17 1015
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081117HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.781740HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d225SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes52HARMONIC5
X-RAY DIFFRACTIONt_it1117HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion184SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact503SEMIHARMONIC4
X-RAY DIFFRACTIONt_other_torsion22.06
LS refinement shellResolution: 2.63→2.91 Å
RfactorNum. reflection% reflection
Rfree0.358 27 -
Rwork0.3545 --
obs0.3547 442 18.29 %
Refinement TLS params.Origin x: -7.7492 Å / Origin y: -16.8967 Å / Origin z: -22.7353 Å
111213212223313233
T0.0834 Å20.0675 Å2-0.1264 Å2-0.1572 Å2-0.304 Å2---0.0411 Å2
L3.7794 °21.3143 °2-0.8778 °2-4.6409 °25.8208 °2--3.7297 °2
S-0.14 Å °0.1432 Å °0.4717 Å °0.1432 Å °0.9302 Å °0.4088 Å °0.4717 Å °0.4088 Å °-0.7903 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 46
2X-RAY DIFFRACTION1{ A|* }A102

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