[English] 日本語
Yorodumi
- PDB-6hc5: The structure of the G. violaceus guanidine II riboswitch P2 stem... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hc5
TitleThe structure of the G. violaceus guanidine II riboswitch P2 stem-loop with audouine
ComponentsRNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
KeywordsRNA / guanidine II riboswitch / stem-loop / tetra loop / dimer
Function / homology1-(5-carbamimidamidopentyl)guanidine / RNA / RNA (> 10)
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.413 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
CitationJournal: Rna / Year: 2019
Title: Structure-guided design of a high-affinity ligand for a riboswitch.
Authors: Huang, L. / Wang, J. / Wilson, T.J. / Lilley, D.M.J.
History
DepositionAug 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 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: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2326
Polymers5,8801
Non-polymers3515
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.826, 55.826, 133.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-105-

FXT

21A-218-

HOH

31A-225-

HOH

41A-226-

HOH

51A-227-

HOH

61A-245-

HOH

-
Components

#1: RNA chain RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3')


Mass: 5880.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gloeobacter violaceus (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FXT / 1-(5-carbamimidamidopentyl)guanidine


Mass: 186.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.01 M Magnesium Acetate, 0.05 M MES pH 5.0, 2.5 M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9196 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 1.413→27.913 Å / Num. obs: 28892 / % possible obs: 98 % / Observed criterion σ(I): 0.8 / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.021 / Net I/σ(I): 18.1
Reflection shellResolution: 1.413→1.437 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.92 / Num. unique obs: 775 / CC1/2: 0.428 / Rpim(I) all: 0.813 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3228: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementResolution: 1.413→27.913 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.1
RfactorNum. reflection% reflection
Rfree0.1989 1467 5.08 %
Rwork0.1754 --
obs0.1765 28892 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.413→27.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 375 21 45 441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012434
X-RAY DIFFRACTIONf_angle_d1.801670
X-RAY DIFFRACTIONf_dihedral_angle_d16.631211
X-RAY DIFFRACTIONf_chiral_restr0.06887
X-RAY DIFFRACTIONf_plane_restr0.01517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4125-1.4630.41481740.36832733X-RAY DIFFRACTION98
1.463-1.52160.34821250.30092865X-RAY DIFFRACTION100
1.5216-1.59080.30231720.24192750X-RAY DIFFRACTION99
1.5908-1.67470.24651310.20472800X-RAY DIFFRACTION99
1.6747-1.77960.16881040.17622864X-RAY DIFFRACTION98
1.7796-1.91690.21561590.16582792X-RAY DIFFRACTION100
1.9169-2.10980.23241550.17222490X-RAY DIFFRACTION89
2.1098-2.41490.19161480.17912605X-RAY DIFFRACTION92
2.4149-3.0420.17821790.19622754X-RAY DIFFRACTION99
3.042-27.91840.18891200.15562772X-RAY DIFFRACTION97

+
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