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- PDB-7qsh: 23S ribosomal RNA Sarcin Ricin Loop 27-nt fragment containing a X... -

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Basic information

Entry
Database: PDB / ID: 7qsh
Title23S ribosomal RNA Sarcin Ricin Loop 27-nt fragment containing a Xanthosine residue at position 2648
Components23S ribosomal RNA Sarcin Ricin Loop 27-nucleotide fragment
KeywordsRNA / modified base
Function / homologyChem-HYJ / URIDINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 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 13, 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 1.2Feb 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: 23S ribosomal RNA Sarcin Ricin Loop 27-nucleotide fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3305
Polymers8,5331
Non-polymers7974
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.500, 29.500, 76.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 23S ribosomal RNA Sarcin Ricin Loop 27-nucleotide fragment


Mass: 8533.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 151 molecules

#2: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Chemical ChemComp-HYJ / 9-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-2-oxidanyl-1~{H}-purin-6-one


Type: L-RNA linking / Mass: 364.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.95 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, magnesium acetate, MES pH5.6

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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: 0.86→50 Å / Num. obs: 54707 / % possible obs: 98.9 % / Redundancy: 20 % / Biso Wilson estimate: 7.88 Å2 / CC1/2: 1 / Net I/σ(I): 56
Reflection shellResolution: 0.86→0.88 Å / Num. unique obs: 3549 / CC1/2: 0.049

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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: 3DVZ

3dvz


Resolution: 0.86→29.5 Å / SU ML: 0.094 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1663 2736 5 %
Rwork0.1466 51969 -
obs0.1476 54705 98.94 %
Solvent computationShrinkage radii: 0.4 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.38 Å2
Refinement stepCycle: LAST / Resolution: 0.86→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 539 51 147 737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051918
X-RAY DIFFRACTIONf_angle_d1.42131427
X-RAY DIFFRACTIONf_chiral_restr0.0449186
X-RAY DIFFRACTIONf_plane_restr0.019840
X-RAY DIFFRACTIONf_dihedral_angle_d10.9542434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.86-0.870.3331160.34972202X-RAY DIFFRACTION83.44
0.87-0.890.3071340.29522544X-RAY DIFFRACTION96.12
0.89-0.910.25991350.25932573X-RAY DIFFRACTION99.34
0.91-0.930.23191390.22712638X-RAY DIFFRACTION100
0.93-0.950.21811380.21562610X-RAY DIFFRACTION100
0.95-0.970.25631360.21282599X-RAY DIFFRACTION100
0.97-0.990.22391400.20522642X-RAY DIFFRACTION100
0.99-1.020.18311380.18772637X-RAY DIFFRACTION100
1.02-1.050.18661380.18062622X-RAY DIFFRACTION100
1.05-1.080.18231370.16982595X-RAY DIFFRACTION100
1.08-1.120.15821390.16262633X-RAY DIFFRACTION100
1.12-1.170.14561360.15712599X-RAY DIFFRACTION100
1.17-1.220.16791400.15152647X-RAY DIFFRACTION100
1.22-1.280.14661380.1482621X-RAY DIFFRACTION100
1.28-1.370.16451370.1512618X-RAY DIFFRACTION100
1.37-1.470.16731390.15222642X-RAY DIFFRACTION100
1.47-1.620.14641380.13682609X-RAY DIFFRACTION100
1.62-1.850.13171390.1222644X-RAY DIFFRACTION100
1.85-2.330.17191380.13462633X-RAY DIFFRACTION100
2.33-29.50.15981410.12192661X-RAY DIFFRACTION99.93

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