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

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Magnesium sulfate, TRIS HCl, Ammonium sulfate

-
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

-
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

+
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