[English] 日本語
Yorodumi
- PDB-6dn1: CRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1151 SPLIT RNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dn1
TitleCRYSTAL STRUCTURE OF THE FMN RIBOSWITCH BOUND TO BRX1151 SPLIT RNA
Components
  • RNA (57-MER)
  • RNA RIBOSWITCH
KeywordsRNA / FMN / RIBOSWITCH / TRANSCRIPTION
Function / homologyChem-GZ7 / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsVicens, Q. / Mondragon, E. / Reyes, F.E. / Berman, J. / Kaur, H. / Kells, K. / Wickens, P. / Wilson, J. / Gadwood, R. / Schostarez, H. ...Vicens, Q. / Mondragon, E. / Reyes, F.E. / Berman, J. / Kaur, H. / Kells, K. / Wickens, P. / Wilson, J. / Gadwood, R. / Schostarez, H. / Suto, R.K. / Coish, P. / Blount, K.F. / Batey, R.T.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch.
Authors: Vicens, Q. / Mondragon, E. / Reyes, F.E. / Coish, P. / Aristoff, P. / Berman, J. / Kaur, H. / Kells, K.W. / Wickens, P. / Wilson, J. / Gadwood, R.C. / Schostarez, H.J. / Suto, R.K. / Blount, K.F. / Batey, R.T.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 21, 2020Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Oct 11, 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 RIBOSWITCH
Z: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,54210
Polymers35,9162
Non-polymers6258
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-48 kcal/mol
Surface area16650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.440, 74.440, 140.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
RNA chain , 2 types, 2 molecules XZ

#1: RNA chain RNA RIBOSWITCH


Mass: 17415.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria)
#2: RNA chain RNA (57-MER)


Mass: 18501.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Fusobacterium nucleatum (bacteria)

-
Non-polymers , 4 types, 36 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GZ7 / 10-(6-carboxyhexyl)-8-(cyclopentylamino)-2,4-dihydroxy-7-methylbenzo[g]pteridin-10-ium


Mass: 440.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 6.5 / Details: PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→140.711 Å / Num. obs: 36651 / % possible obs: 67 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 80 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.111 / Χ2: 1.198 / Net I/σ(I): 6.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Num. unique obs% possible allMean I/σ(I) obsCC1/2Rmerge(I) obsRrim(I) all
2.05-2.17135015.4
2.17-2.32361643.40.020.226
2.32-2.51495363.9
2.51-2.75583481.90.17.6319.191
2.75-3.07607594.40.910.4211.611.839
3.07-3.55528693.15.320.9540.2960.341
3.55-4.34437091.213.360.9920.1060.122
4.34-6.12336390.524.890.9970.0480.055
6.12-140.711180487.930.470.9980.0350.04

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F4E

3f4e


Resolution: 3.03→30.88 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.404
RfactorNum. reflection% reflectionSelection details
Rfree0.242 471 5.27 %RANDOM
Rwork0.223 ---
obs0.224 8941 97 %-
Displacement parametersBiso max: 137.84 Å2 / Biso mean: 84.76 Å2 / Biso min: 50.69 Å2
Baniso -1Baniso -2Baniso -3
1-4.0653 Å20 Å20 Å2
2--4.0653 Å20 Å2
3----8.1306 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 3.03→30.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2384 68 28 2480
Biso mean--67.73 70.4 -
Num. residues----111
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d564SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes143HARMONIC5
X-RAY DIFFRACTIONt_it2733HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion444SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2740SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2733HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4275HARMONIC20.77
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion26.69
LS refinement shellResolution: 3.03→3.39 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.275 146 5.75 %
Rwork0.263 2395 -
all-2541 -
obs--98.95 %

+
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