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

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Basic information

Entry
Database: PDB / ID: 7qua
TitleDuplex RNA containing Xanthosine-Cytosine base pairs
ComponentsRNA (5'-R(*CP*GP*CP*GP*(XAN)P*AP*UP*UP*AP*GP*CP*G)-3')
KeywordsRNA / modified base
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 17, 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 1.2Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*GP*(XAN)P*AP*UP*UP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9645
Polymers3,8691
Non-polymers954
Water1,946108
1
A: RNA (5'-R(*CP*GP*CP*GP*(XAN)P*AP*UP*UP*AP*GP*CP*G)-3')
hetero molecules

A: RNA (5'-R(*CP*GP*CP*GP*(XAN)P*AP*UP*UP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,92810
Polymers7,7392
Non-polymers1898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3600 Å2
ΔGint-69 kcal/mol
Surface area3930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.070, 35.150, 31.930
Angle α, β, γ (deg.)90.000, 129.052, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 3869.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Na cacodylate pH7.0, MPD, spermine, NaCl, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.96→50 Å / Num. obs: 220228 / % possible obs: 90 % / Redundancy: 11.2 % / Biso Wilson estimate: 9.34 Å2 / CC1/2: 1 / Net I/σ(I): 18.9
Reflection shellResolution: 0.96→0.98 Å / Num. unique obs: 470 / CC1/2: 0.05

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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: 2Q1R

2q1r


Resolution: 1→24.8 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1576 934 5.01 %
Rwork0.1374 17722 -
obs0.1384 18656 97.44 %
Solvent computationShrinkage radii: 0.4 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.57 Å2
Refinement stepCycle: LAST / Resolution: 1→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 256 4 108 368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115305
X-RAY DIFFRACTIONf_angle_d1.4911475
X-RAY DIFFRACTIONf_chiral_restr0.044462
X-RAY DIFFRACTIONf_plane_restr0.037714
X-RAY DIFFRACTIONf_dihedral_angle_d6.6126143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.050.58141120.56292120X-RAY DIFFRACTION82.33
1.05-1.120.28861370.24012593X-RAY DIFFRACTION99.89
1.12-1.210.15761350.14282568X-RAY DIFFRACTION100
1.21-1.330.11991370.12312600X-RAY DIFFRACTION100
1.33-1.520.151360.12962600X-RAY DIFFRACTION100
1.52-1.910.13411370.12092597X-RAY DIFFRACTION99.82
1.91-24.80.14551400.11862644X-RAY DIFFRACTION99.93

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