[English] 日本語
Yorodumi
- PDB-7tda: Crystal structure of the E. coli thiM riboswitch in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tda
TitleCrystal structure of the E. coli thiM riboswitch in complex with thiamine pyrophosphate, manganese ions
ComponentsthiM TPP riboswitch RNA (80-MER)
KeywordsRNA
Function / homology: / THIAMINE DIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNuthanakanti, A. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112940 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.
Authors: Zeller, M.J. / Nuthanakanti, A. / Li, K. / Aube, J. / Serganov, A. / Weeks, K.M.
History
DepositionDec 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: thiM TPP riboswitch RNA (80-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,92617
Polymers26,8611
Non-polymers1,06616
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.410, 65.410, 101.504
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

-
Components

#1: RNA chain thiM TPP riboswitch RNA (80-MER)


Mass: 26860.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.29 % / Description: Rod-shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 0.5 mM of TPP. the reservoir solution was 50 mM Bis-Tris ...Details: RNA (0.15 mM) was incubated in a buffer containing 5 mM Tris-HCl, pH 8.0, 3 mM MgCl2, 10 mM NaCl, 0.1 M KCl, and 0.5 mM spermine with 0.5 mM of TPP. the reservoir solution was 50 mM Bis-Tris HCl, pH 6.5, 0.5 M NH4Cl, 10 mm MnCl2, and 30% (v/v) PEG2000
PH range: 6.0-6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 12071 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Net I/σ(I): 82.7
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.297 / Mean I/σ(I) obs: 1 / Num. unique obs: 589 / CC1/2: 0.7 / Rpim(I) all: 0.437 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HOJ

2hoj


Resolution: 2.25→29.05 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 2311 10.01 %
Rwork0.2089 --
obs0.2112 12071 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1664 34 33 1731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041910
X-RAY DIFFRACTIONf_angle_d0.9512971
X-RAY DIFFRACTIONf_dihedral_angle_d16.233935
X-RAY DIFFRACTIONf_chiral_restr0.048384
X-RAY DIFFRACTIONf_plane_restr0.00778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.53071320.45321170X-RAY DIFFRACTION98
2.29-2.340.41881460.38221247X-RAY DIFFRACTION100
2.34-2.40.36241400.34261232X-RAY DIFFRACTION100
2.4-2.460.391320.33761205X-RAY DIFFRACTION100
2.46-2.520.36791300.27941229X-RAY DIFFRACTION100
2.53-2.60.3341260.29351224X-RAY DIFFRACTION100
2.6-2.680.32681380.31911231X-RAY DIFFRACTION100
2.68-2.780.33481360.32151223X-RAY DIFFRACTION100
2.78-2.890.3291380.3061195X-RAY DIFFRACTION100
2.89-3.020.2921350.26971250X-RAY DIFFRACTION100
3.02-3.180.2281420.23251232X-RAY DIFFRACTION100
3.18-3.380.2171340.21081212X-RAY DIFFRACTION100
3.38-3.640.2411440.19221222X-RAY DIFFRACTION100
3.64-4.010.20151380.17861227X-RAY DIFFRACTION100
4.01-4.580.18551360.1691208X-RAY DIFFRACTION100
4.58-5.760.16151280.16261232X-RAY DIFFRACTION100
5.77-29.050.20681360.1651228X-RAY DIFFRACTION100

+
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