[English] 日本語
Yorodumi
- PDB-6wjr: Apo structure of the FMN riboswitch aptamer domain in the presenc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wjr
TitleApo structure of the FMN riboswitch aptamer domain in the presence of sulfate
ComponentsRNA (112-MER)
KeywordsRNA / riboswitch / RNA conformation / apo
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWilt, H.M. / Wang, Y.-X. / Stagno, J.R.
CitationJournal: J Struct Biol X / Year: 2020
Title: FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations.
Authors: Wilt, H.M. / Yu, P. / Tan, K. / Wang, Y.X. / Stagno, J.R.
History
DepositionApr 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Structure summary / Category: audit_author
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 18, 2023Group: 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
X: RNA (112-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3503
Polymers36,2291
Non-polymers1202
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.635, 36.468, 205.524
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: RNA chain RNA (112-MER)


Mass: 36229.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria) / References: GenBank: 929732263
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, and 26 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033175 Å / Relative weight: 1
ReflectionResolution: 2.7→42.14 Å / Num. obs: 15928 / % possible obs: 99 % / Redundancy: 4.046 % / Biso Wilson estimate: 104.085 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.104 / Χ2: 0.834 / Net I/σ(I): 8.16 / Num. measured all: 64444
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.774.2944.7930.335015117311680.1385.44799.6
2.77-2.854.2813.0270.514825113211270.233.44299.6
2.85-2.934.1552.3360.74508108610850.252.67299.9
2.93-3.023.9321.4091.14239108410780.4871.61799.4
3.02-3.124.1640.8161.94272102710260.7930.93399.9
3.12-3.234.2810.4393.334281100210000.940.599.8
3.23-3.354.310.2844.75429710019970.9770.32399.6
3.35-3.494.3220.2635.4939379139110.9780.399.8
3.49-3.644.1190.1946.637699249150.980.22399
3.64-3.824.2150.143935708498470.9880.16499.8
3.82-4.023.8660.11910.5431978378270.9870.13998.8
4.02-4.273.7690.09912.8128837747650.9840.11798.8
4.27-4.563.6160.08414.5827777787680.990.09898.7
4.56-4.934.0060.06917.7926686736660.9920.08199
4.93-5.44.0060.06619.4225206466290.9930.07697.4
5.4-6.043.9210.06220.3722825955820.9930.07297.8
6.04-6.973.8050.05520.7419715295180.9940.06497.9
6.97-8.543.3750.04920.9314854554400.9910.05996.7
8.54-12.073.470.04422.3212843813700.9950.05297.1
12.07-42.143.1770.04321.586642332090.9990.05189.7

-
Processing

Software
NameVersionClassification
PHENIX1.18rc5_3822refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F2Q

3f2q


Resolution: 2.7→42.14 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 727 4.67 %
Rwork0.2206 14853 -
obs0.2222 15580 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 261.26 Å2 / Biso mean: 118.0549 Å2 / Biso min: 66.8 Å2
Refinement stepCycle: final / Resolution: 2.7→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2382 6 2 2390
Biso mean--90.13 76.52 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062671
X-RAY DIFFRACTIONf_angle_d1.3854165
X-RAY DIFFRACTIONf_dihedral_angle_d16.6581329
X-RAY DIFFRACTIONf_chiral_restr0.096555
X-RAY DIFFRACTIONf_plane_restr0.008111
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.80.5857600.47321249130982
2.8-2.910.4808730.464614711544100
2.91-3.040.3635900.38021500159099
3.04-3.20.245680.275914791547100
3.2-3.40.2559590.26271491155099
3.4-3.660.2527830.22791502158599
3.66-4.030.3014750.22041497157299
4.03-4.620.1723790.19261509158899
4.62-5.810.1989770.1821530160799
5.81-42.140.3002630.20351625168896
Refinement TLS params.Method: refined / Origin x: 11.14 Å / Origin y: -14.882 Å / Origin z: -30.679 Å
111213212223313233
T1.0823 Å20.0257 Å20.1485 Å2-0.9913 Å20.1038 Å2--0.9917 Å2
L2.9108 °20.9563 °2-0.6492 °2-2.8371 °2-0.2562 °2--2.072 °2
S0.2585 Å °-0.8568 Å °0.4733 Å °0.7003 Å °-0.01 Å °0.5371 Å °-0.3282 Å °-0.0992 Å °0.0001 Å °
Refinement TLS groupSelection details: ( CHAIN X AND RESID 1:111 )

+
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://pdbjlvh1.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