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- PDB-7qtn: Duplex RNA containing Xanthosine-Cytosine base pairs -

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Basic information

Entry
Database: PDB / ID: 7qtn
TitleDuplex RNA containing Xanthosine-Cytosine base pairs
Components
  • RNA (5'-R(*GP*GP*UP*AP*(RY)P*UP*GP*CP*GP*(XAN)P*UP*AP*CP*C)-3')
  • RNA (5'-R(*GP*GP*UP*AP*CP*UP*GP*CP*GP*(XAM)P*UP*AP*CP*C)-3')
KeywordsRNA / modified base
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsEnnifar, E. / Micura, R.
Funding support Austria, 5items
OrganizationGrant numberCountry
Austrian Science FundP31691 Austria
Austrian Science FundF8011-B Austria
Austrian Science FundP32773 Austria
Austrian Science FundP30087 Austria
Austrian Research Promotion AgencyWest Austrian BioNMR 858017 Austria
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA.
Authors: Mair, S. / Erharter, K. / Renard, E. / Brillet, K. / Brunner, M. / Lusser, A. / Kreutz, C. / Ennifar, E. / Micura, R.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*UP*AP*(RY)P*UP*GP*CP*GP*(XAN)P*UP*AP*CP*C)-3')
B: RNA (5'-R(*GP*GP*UP*AP*CP*UP*GP*CP*GP*(XAM)P*UP*AP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,9622
Polymers8,9622
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.880, 44.880, 149.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

21A-120-

HOH

31A-125-

HOH

41A-140-

HOH

51A-141-

HOH

61A-148-

HOH

71A-149-

HOH

81B-131-

HOH

91B-134-

HOH

101B-159-

HOH

111B-166-

HOH

121B-167-

HOH

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Components

#1: RNA chain RNA (5'-R(*GP*GP*UP*AP*(RY)P*UP*GP*CP*GP*(XAN)P*UP*AP*CP*C)-3')


Mass: 4481.706 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*GP*GP*UP*AP*CP*UP*GP*CP*GP*(XAM)P*UP*AP*CP*C)-3')


Mass: 4480.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Magnesium sulfate, TRIS HCl, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 1894942 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 1 / Net I/σ(I): 32.3
Reflection shellResolution: 1.2→1.23 Å / Num. unique obs: 68877 / CC1/2: 0.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 433D

433d


Resolution: 1.2→38.87 Å / SU ML: 0.2268 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 1449 5 %
Rwork0.1825 27532 -
obs0.1838 28981 99.81 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.41 Å2
Refinement stepCycle: LAST / Resolution: 1.2→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 592 0 121 713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079660
X-RAY DIFFRACTIONf_angle_d1.09851026
X-RAY DIFFRACTIONf_chiral_restr0.0453135
X-RAY DIFFRACTIONf_plane_restr0.013228
X-RAY DIFFRACTIONf_dihedral_angle_d6.7511303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.41971410.3762687X-RAY DIFFRACTION100
1.24-1.290.3531410.34962680X-RAY DIFFRACTION99.96
1.29-1.350.33341420.28042684X-RAY DIFFRACTION100
1.35-1.420.2851420.2382696X-RAY DIFFRACTION100
1.42-1.510.23521430.19752715X-RAY DIFFRACTION99.97
1.51-1.630.21581420.16122724X-RAY DIFFRACTION99.72
1.63-1.790.17921440.13762725X-RAY DIFFRACTION99.27
1.79-2.050.16451460.15062779X-RAY DIFFRACTION100
2.05-2.590.20181480.18012811X-RAY DIFFRACTION99.97
2.59-38.870.20211600.17873031X-RAY DIFFRACTION99.28

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