[English] 日本語
Yorodumi
- PDB-4lvx: Structure of the THF riboswitch bound to tetrahydrobiopterin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lvx
TitleStructure of the THF riboswitch bound to tetrahydrobiopterin
ComponentsTHF riboswitch
KeywordsRNA / Aptamers / Nucleotide / Bacillus subtilis / Bacterial Proteins / Base Sequence / Binding Sites / Calorimetry / Folic Acid / Gene Expression Regulation / Bacterial / Guanine / Leucovorin / Ligands / Magnesium / Molecular Sequence Data / Nucleic Acid Conformation / Point Mutation / Protein Binding / Protein Structure / Secondary / Riboswitch / S-Adenosylmethionine / Streptococcus mutans / Terminator Regions / Genetic / Tetrahydrofolates / Thermodynamics / Transcription / three-way junction / pseudoknot / regulation / ncRNA / tetrahydrobiopterin binding / mRNA
Function / homology5,6,7,8-TETRAHYDROBIOPTERIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTrausch, J.J. / Batey, R.T.
Citation
Journal: Chem.Biol. / Year: 2014
Title: A Disconnect between High-Affinity Binding and Efficient Regulation by Antifolates and Purines in the Tetrahydrofolate Riboswitch.
Authors: Trausch, J.J. / Batey, R.T.
#1: Journal: Structure / Year: 2011
Title: The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.
Authors: Trausch, J.J. / Ceres, P. / Reyes, F.E. / Batey, R.T.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THF riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3323
Polymers28,8491
Non-polymers4822
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.990, 68.620, 158.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: RNA chain THF riboswitch


Mass: 28849.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 in vitro transcribed
#2: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2,4-methyl-pentanediol, spermine, sodium cacodylate, sodium chloride, dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1051 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1051 Å / Relative weight: 1
ReflectionResolution: 1.9→52.69 Å / Num. all: 24030 / % possible obs: 99.4 % / Observed criterion σ(F): 5.5 / Observed criterion σ(I): 5.5 / Redundancy: 5.7 %
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.109 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.751 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 1199 5.01 %
Rwork0.2204 --
obs0.2215 23940 99.16 %
all-24030 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→28.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1913 34 168 2115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042178
X-RAY DIFFRACTIONf_angle_d0.9773392
X-RAY DIFFRACTIONf_dihedral_angle_d11.9671075
X-RAY DIFFRACTIONf_chiral_restr0.044451
X-RAY DIFFRACTIONf_plane_restr0.00791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97610.35971280.30852445X-RAY DIFFRACTION99
1.9761-2.0660.35311330.28312495X-RAY DIFFRACTION100
2.066-2.17490.28731300.2692484X-RAY DIFFRACTION100
2.1749-2.31110.28851330.26642523X-RAY DIFFRACTION100
2.3111-2.48940.32571330.27292521X-RAY DIFFRACTION100
2.4894-2.73980.28241330.27032547X-RAY DIFFRACTION100
2.7398-3.13580.28461340.24352519X-RAY DIFFRACTION100
3.1358-3.94920.22221360.19232588X-RAY DIFFRACTION99
3.9492-28.75440.17891390.18572619X-RAY DIFFRACTION95

+
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