[English] 日本語
Yorodumi
- PDB-5nqi: E.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nqi
TitleE.coli 16S rRNA Sarcin-Ricin Loop containing a 5-hydroxymethylcytosine modification
ComponentsE.Coli 27-mer SRL RNA
KeywordsRNA / modification
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.851 Å
AuthorsEnnifar, E. / Micura, R.
CitationJournal: J. Org. Chem. / Year: 2017
Title: Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine.
Authors: Riml, C. / Lusser, A. / Ennifar, E. / Micura, R.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E.Coli 27-mer SRL RNA


Theoretical massNumber of molelcules
Total (without water)8,7741
Polymers8,7741
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.510, 29.510, 76.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: RNA chain E.Coli 27-mer SRL RNA


Mass: 8774.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 3.0-3.2 M (NH4)2SO4, 50 mM KMops (pH 7.0), 10 mM MgCl2, 10 mM MnCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.77491 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77491 Å / Relative weight: 1
ReflectionResolution: 0.85→50 Å / Num. obs: 1277131 / % possible obs: 99.6 % / Redundancy: 22 % / Net I/σ(I): 30

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 0.851→29.51 Å / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 19.87
RfactorNum. reflection% reflection
Rfree0.1704 2870 5.03 %
Rwork0.1458 --
obs0.1737 57106 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.851→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 581 0 211 792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006707
X-RAY DIFFRACTIONf_angle_d1.1241107
X-RAY DIFFRACTIONf_dihedral_angle_d12.481347
X-RAY DIFFRACTIONf_chiral_restr0.047147
X-RAY DIFFRACTIONf_plane_restr0.01330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8509-0.86550.46021360.42842577X-RAY DIFFRACTION89
0.8655-0.88130.41621390.38112649X-RAY DIFFRACTION93
0.8813-0.89820.36761430.35672711X-RAY DIFFRACTION95
0.8982-0.91660.33581430.33862720X-RAY DIFFRACTION95
0.9166-0.93650.31991420.3032694X-RAY DIFFRACTION95
0.9365-0.95830.27691450.2852751X-RAY DIFFRACTION95
0.9583-0.98220.25931430.24442721X-RAY DIFFRACTION95
0.9822-1.00880.21251420.22112687X-RAY DIFFRACTION95
1.0088-1.03850.21371430.20152732X-RAY DIFFRACTION95
1.0385-1.0720.19681420.19132699X-RAY DIFFRACTION95
1.072-1.11030.19841440.19162725X-RAY DIFFRACTION95
1.1103-1.15480.18681430.18922721X-RAY DIFFRACTION95
1.1548-1.20730.20631430.18762722X-RAY DIFFRACTION95
1.2073-1.2710.17041440.18712740X-RAY DIFFRACTION95
1.271-1.35060.17721450.18162736X-RAY DIFFRACTION95
1.3506-1.45490.19571410.17632695X-RAY DIFFRACTION95
1.4549-1.60130.16391450.16952740X-RAY DIFFRACTION95
1.6013-1.8330.15751440.14752740X-RAY DIFFRACTION95
1.833-2.30920.16951430.15112725X-RAY DIFFRACTION95
2.3092-27.56090.19141460.12572761X-RAY DIFFRACTION95

+
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