[English] 日本語
Yorodumi
- PDB-3gx2: TteSAM-I riboswitch variant A94GU34C bound to sinefungin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gx2
TitleTteSAM-I riboswitch variant A94GU34C bound to sinefungin
ComponentsRNA (94-MER)
KeywordsRNA / kink-turn / pseudoknot / four-way junction
Function / homologySINEFUNGIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMontange, R.K. / Batey, R.T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch.
Authors: Montange, R.K. / Mondragon, E. / van Tyne, D. / Garst, A.D. / Ceres, P. / Batey, R.T.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (94-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1209
Polymers30,5681
Non-polymers5528
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)62.614, 62.614, 158.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: RNA chain RNA (94-MER)


Mass: 30568.338 Da / Num. of mol.: 1 / Mutation: U34C, A94G / Source method: obtained synthetically
Details: This sequence is based on a sequence found in T. tengcongensis
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30 mM magnesium chloride, 60 mM potassium chloride, 12 mM spermine-HCl, 10% MPD, 40 mM cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2potassium chloride11
3spermine-HCl11
4MPD11
5cacodylateCacodylic acid11
6magnesium chloride12
7potassium chloride12
8spermine-HCl12
9MPD12
10cacodylateCacodylic acid12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 21, 2009
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 7451 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.64 % / Biso Wilson estimate: 68.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.53 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.7 / Num. unique all: 7500 / % possible all: 100

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GIS
Resolution: 2.9→19.41 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 729 9.94 %
Rwork0.2219 --
obs0.2283 7333 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.845 Å2 / ksol: 0.273 e/Å3
Displacement parametersBiso mean: 68.1 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2030 34 0 2064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_d2.17
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_dihedral_angle_d28.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.12310.41781440.29751265X-RAY DIFFRACTION97
3.1231-3.43580.29241430.23381288X-RAY DIFFRACTION98
3.4358-3.92940.29341410.21041309X-RAY DIFFRACTION98
3.9294-4.93710.28311510.20631334X-RAY DIFFRACTION99
4.9371-19.41010.23631500.19631408X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 52.2028 Å / Origin y: 52.9523 Å / Origin z: 23.4011 Å
111213212223313233
T0.2685 Å20.0307 Å2-0.0188 Å2-0.1915 Å2-0.1193 Å2--0.2744 Å2
L1.2897 °21.611 °20.0771 °2-0.0399 °20.8401 °2--2.8657 °2
S0.3729 Å °-0.1506 Å °-0.024 Å °-0.2171 Å °0.0324 Å °-0.0196 Å °-0.0905 Å °0.1627 Å °-0.3089 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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