[English] 日本語
Yorodumi
- PDB-6zxz: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zxz
TitleSarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
ComponentsSarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
KeywordsRNA / Ribosome / modification
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsEnnifar, E.
Funding support Austria, 3items
OrganizationGrant numberCountry
Austrian Science FundP27947 Austria
Austrian Science FundP31691 Austria
Austrian Research Promotion AgencyWest Austrian BioNMR 858017 Austria
Citation
Journal: Chem Sci / Year: 2020
Title: 2'- O -Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy.
Authors: Himmelstoss, M. / Erharter, K. / Renard, E. / Ennifar, E. / Kreutz, C. / Micura, R.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.
History
DepositionJul 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
B: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
C: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,71911
Polymers25,4703
Non-polymers2488
Water91951
1
A: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5914
Polymers8,4901
Non-polymers1013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5523
Polymers8,4901
Non-polymers622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5754
Polymers8,4901
Non-polymers853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.412, 75.267, 52.981
Angle α, β, γ (deg.)90.000, 105.604, 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 Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification


Mass: 8490.089 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: RNA 1 volume Buffer (NaCl 80 mM, KCl 12 mM, MgCl2 20 mM, NaCaco pH7.0 40 mM, MPD 35 %, spermine tetrahydrochloride 12 mM) 1 volume

-
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: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 17179 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.53 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.23
Reflection shellResolution: 2.44→2.59 Å / Num. unique obs: 2748 / CC1/2: 0.359

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS31 Jan 2020data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVZ

3dvz


Resolution: 2.44→46.97 Å / SU ML: 0.3907 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.3476
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 858 5 %
Rwork0.2106 16288 -
obs0.212 17146 99.47 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 2.44→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1698 8 51 1757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00181899
X-RAY DIFFRACTIONf_angle_d0.53082961
X-RAY DIFFRACTIONf_chiral_restr0.0242387
X-RAY DIFFRACTIONf_plane_restr0.003478
X-RAY DIFFRACTIONf_dihedral_angle_d12.2058906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.590.36571420.35852711X-RAY DIFFRACTION98.75
2.59-2.790.35881420.32112682X-RAY DIFFRACTION99.79
2.79-3.080.31811420.26632739X-RAY DIFFRACTION99.97
3.08-3.520.22261460.21112717X-RAY DIFFRACTION99
3.52-4.430.20551430.16442727X-RAY DIFFRACTION99.55
4.44-46.970.16331430.15922712X-RAY DIFFRACTION99.76

+
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