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- PDB-6qn3: Structure of the Glutamine II Riboswitch -

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Basic information

Entry
Database: PDB / ID: 6qn3
TitleStructure of the Glutamine II Riboswitch
ComponentsRNA (51-MER)
KeywordsRNA / Glutamine II Riboswitch / stem-loop / tetra loop / dimer / gene regulation
Function / homologyBROMIDE ION / GLUTAMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesProchlorococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structure and ligand binding of the glutamine-II riboswitch.
Authors: Huang, L. / Wang, J. / Watkins, A.M. / Das, R. / Lilley, D.M.J.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (51-MER)
B: RNA (51-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,04812
Polymers32,3392
Non-polymers70910
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-35 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.502, 115.725, 80.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

#1: RNA chain RNA (51-MER)


Mass: 16169.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Prochlorococcus sp. (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M Magnesium Acetate tetrahydrate 0.1 M Sodium Cacodylate pH 6.0 19% Polyethylene Glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9195 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2.2→80.58 Å / Num. obs: 36523 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Net I/σ(I): 8.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.639 / Num. unique obs: 938 / CC1/2: 0.762 / Rpim(I) all: 0.762 / % possible all: 99.58

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.001 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.51
RfactorNum. reflection% reflection
Rfree0.2944 1566 5.13 %
Rwork0.2424 --
obs0.2451 30523 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2160 8 18 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082412
X-RAY DIFFRACTIONf_angle_d1.5133754
X-RAY DIFFRACTIONf_dihedral_angle_d18.0971200
X-RAY DIFFRACTIONf_chiral_restr0.072500
X-RAY DIFFRACTIONf_plane_restr0.01104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37420.42241510.40612646X-RAY DIFFRACTION100
2.3742-2.45910.46381450.41312596X-RAY DIFFRACTION100
2.4591-2.55760.40661220.41592662X-RAY DIFFRACTION99
2.5576-2.67390.41221460.39932656X-RAY DIFFRACTION100
2.6739-2.81490.52271400.39662609X-RAY DIFFRACTION99
2.8149-2.99120.45811540.35132631X-RAY DIFFRACTION100
2.9912-3.22210.3431460.28762605X-RAY DIFFRACTION98
3.2221-3.54630.34731340.22522624X-RAY DIFFRACTION99
3.5463-4.05920.23931350.182648X-RAY DIFFRACTION99
4.0592-5.11320.17411300.16392648X-RAY DIFFRACTION100
5.1132-47.01060.20961630.172632X-RAY DIFFRACTION100

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