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- PDB-7uq6: tRNA T-box antiterminator fusion, construct #4 -

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Basic information

Entry
Database: PDB / ID: 7uq6
TitletRNA T-box antiterminator fusion, construct #4
ComponentsRNA (86-MER)
KeywordsRNA / tRNA / regulation / riboswitch / scaffold
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.951 Å
AuthorsGrigg, J.C. / Price, I.R. / Ke, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118174 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116632 United States
CitationJournal: Crystals / Year: 2022
Title: tRNA Fusion to Streamline RNA Structure Determination: Case Studies in Probing Aminoacyl-tRNA Sensing Mechanisms by the T-Box Riboswitch
Authors: Grigg, J.C. / Price, I.R. / Ke, A.
History
DepositionApr 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA (86-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,28926
Polymers27,9361
Non-polymers2,35325
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.576, 165.208, 57.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: RNA chain RNA (86-MER)


Mass: 27936.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Description: in vitro transcription / Production host: unidentified (others)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ba
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium cacodylate pH 6.0, 80 mM KCl, 12 mM spermine, 20 mM BaCl2, 15% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.951→32.213 Å / Num. all: 9103 / Num. obs: 9103 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.139 / Rsym value: 0.115 / Net I/av σ(I): 4.6 / Net I/σ(I): 18.9 / Num. measured all: 56484
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.951-3.114.90.5521.212630.2770.6620.55297.5
3.11-3.36.50.354212360.160.4140.354100
3.3-3.526.50.2312.911830.1050.270.23199.9
3.52-3.816.50.1833.510920.0840.2160.183100
3.81-4.176.50.1324.410060.0610.1560.132100
4.17-4.666.50.1025.79230.0470.1210.102100
4.66-5.386.50.0875.88130.0410.1050.087100
5.38-6.596.40.0856.27080.0410.1040.085100
6.59-9.3360.0598.75670.030.0740.059100
9.33-32.2135.50.0539.43120.0320.0750.05395.5

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MGM

4mgm


Resolution: 2.951→32.213 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 434 4.77 %
Rwork0.2466 8659 -
obs0.2475 9093 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.61 Å2 / Biso mean: 63.3193 Å2 / Biso min: 22.11 Å2
Refinement stepCycle: final / Resolution: 2.951→32.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1849 25 0 1874
Biso mean--100.24 --
Num. residues----86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9512-3.37790.33121440.3107279499
3.3779-4.25420.26171450.25722876100
4.2542-32.2130.24181450.22112989100

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