[English] 日本語
Yorodumi
- PDB-7qua: Duplex RNA containing Xanthosine-Cytosine base pairs -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more