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- PDB-3q51: Structural analysis of a class I PreQ1 riboswitch aptamer in the ... -

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Basic information

Entry
Database: PDB / ID: 3q51
TitleStructural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-free state.
ComponentsPREQ1 RIBOSWITCH
KeywordsRNA / PREQ1 / PREQ0 / RIBOSOMAL BINDING SITE / APTAMER / METABOLITE / Pseudoknot / H-type / RIBOSWITCH
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsWedekind, J.E. / Jenkins, J.L. / Krucinska, J.
Citation
Journal: J.Biol.Chem. / Year: 2011
Title: Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation.
Authors: Jenkins, J.L. / Krucinska, J. / McCarty, R.M. / Bandarian, V. / Wedekind, J.E.
#1: Journal: J.Biol.Chem. / Year: 2010
Title: The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain.
Authors: Spitale, R.C. / Torelli, A.T. / Krucinska, J. / Bandarian, V. / Wedekind, J.E.
History
DepositionDec 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 12, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PREQ1 RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7203
Polymers10,5991
Non-polymers1202
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.558, 116.558, 57.926
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: RNA chain PREQ1 RIBOSWITCH


Mass: 10599.417 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The RNA strand was chemically synthesized based on the sequence of a class I, Type 1 PreQ1 riboswitch aptamer from T. tengcongensis
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.358 Å3/Da / Density % sol: 77.044 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 M Li2SO4, 0.2 M MES pH 6.0, 0.02 M Magnesium sulfate, and 0.002 M spermine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2010 / Details: Rh coated flat mirror, toroidal focusing mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 5771 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 70.4 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.292 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.85-2.958.40.3575580.8751100
2.95-3.078.40.2495640.96199.8
3.07-3.218.30.1785621.2371100
3.21-3.387.70.1185631.8451100
3.38-3.597.50.0995701.455199.8
3.59-3.8770.0855771.529199.8
3.87-4.266.80.0745671.422199.6
4.26-4.876.30.0585951.258199.8
4.87-6.145.60.0485921.234199.5
6.14-505.60.0566231.034194.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.4_486phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3GCA

3gca


Resolution: 2.85→27.84 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 561 9.95 %copied R-free set from 3GCA
Rwork0.226 ---
obs0.2306 5639 97.58 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.293 Å2 / ksol: 0.263 e/Å3
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 56.6848 Å2 / Biso min: 34.72 Å2
Baniso -1Baniso -2Baniso -3
1-10.6047 Å20 Å2-0 Å2
2--10.6047 Å20 Å2
3----21.2094 Å2
Refine analyzeLuzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.85→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 680 6 4 690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006764
X-RAY DIFFRACTIONf_angle_d0.8441186
X-RAY DIFFRACTIONf_chiral_restr0.056159
X-RAY DIFFRACTIONf_plane_restr0.00832
X-RAY DIFFRACTIONf_dihedral_angle_d19.382377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-3.13660.36431290.37141210133995
3.1366-3.58970.31311360.23791243137998
3.5897-4.51950.27071430.22941279142299
4.5195-27.8410.24031530.19071346149998

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