[English] 日本語
Yorodumi
- PDB-5nz6: The structure of the thermobifida fusca guanidine III riboswitch ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nz6
TitleThe structure of the thermobifida fusca guanidine III riboswitch with guanidine in space group P3212.
ComponentsRNA (41-MER)
KeywordsRNA / guanidine III riboswitch / stem-loop / pseudoknot / gene regulation
Function / homologyGUANIDINE / RNA / RNA (> 10)
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsHuang, L. / Wang, J. / Lilley, D.M.J.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Structure of the Guanidine III Riboswitch.
Authors: Huang, L. / Wang, J. / Wilson, T.J. / Lilley, D.M.J.
History
DepositionMay 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 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: RNA (41-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4802
Polymers13,4211
Non-polymers591
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-0 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.560, 83.560, 98.814
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

-
Components

#1: RNA chain RNA (41-MER)


Mass: 13420.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermobifida fusca (bacteria)
#2: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% v/v Tacsimate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92019 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 2.94→49.41 Å / Num. obs: 16177 / % possible obs: 100 % / Observed criterion σ(I): 1.7 / Redundancy: 21.57 % / CC1/2: 0.965 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.023 / Net I/σ(I): 18.2
Reflection shellResolution: 2.94→2.99 Å / Redundancy: 21.1 % / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 434 / CC1/2: 0.964 / Rpim(I) all: 0.367 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2219: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NWQ

5nwq


Resolution: 2.94→32.938 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.5
RfactorNum. reflection% reflection
Rfree0.2169 789 4.88 %
Rwork0.1912 --
obs0.1924 16177 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.94→32.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 882 4 0 886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009993
X-RAY DIFFRACTIONf_angle_d1.7211550
X-RAY DIFFRACTIONf_dihedral_angle_d18.285469
X-RAY DIFFRACTIONf_chiral_restr0.07202
X-RAY DIFFRACTIONf_plane_restr0.0142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.12410.46821490.41072488X-RAY DIFFRACTION97
3.1241-3.36510.25671190.22682571X-RAY DIFFRACTION98
3.3651-3.70330.21591520.21012538X-RAY DIFFRACTION99
3.7033-4.23830.20141480.20072551X-RAY DIFFRACTION99
4.2383-5.33610.2228900.16472616X-RAY DIFFRACTION99
5.3361-32.940.17211310.15742624X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0117-1.01-0.7347.8488-0.40220.64860.1168-0.91130.31220.2831-0.09931.1979-0.35610.2593-0.01371.0534-0.448-0.19711.02170.13080.8361-15.9453-11.536713.3855
22.00281.7060.04643.2444-0.34041.4766-0.098-0.4993-0.1275-0.173-0.0857-0.2104-0.35180.42470.22321.1593-0.4348-0.09060.92360.00170.9338-19.9275-19.859215.2363
34.9682-0.3633-1.5917.3736-1.15034.39411.1341-1.0148-0.06330.3373-0.7924-0.3976-0.85610.9552-0.29071.4416-0.4805-0.17270.96450.00291.1012-9.85932.003111.1299
46.75890.7068-3.93191.37260.06838.6557-0.20591.05120.94160.84040.0581-0.7922-0.63380.5787-0.16050.9085-0.5316-0.24161.0174-0.01030.5251-11.9178-1.67224.035
53.10911.0782-1.25531.3616-0.94334.56770.2311-0.4317-0.79380.8089-1.0965-1.23380.7385-0.23330.64690.9279-0.2521-0.1551.05510.25820.8867-5.8553-15.629211.8538
66.6749-0.20940.11446.5967-0.65935.44750.9484-0.5779-0.39420.2163-0.44671.89890.13750.501-0.24361.3779-0.44240.17450.67610.0250.8887-24.7248-21.447420.0191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 25 )
4X-RAY DIFFRACTION4chain 'A' and (resid 26 through 30 )
5X-RAY DIFFRACTION5chain 'A' and (resid 31 through 35 )
6X-RAY DIFFRACTION6chain 'A' and (resid 36 through 41 )

+
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