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- PDB-3q50: Structural analysis of a class I PreQ1 riboswitch aptamer in the ... -

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Basic information

Entry
Database: PDB / ID: 3q50
TitleStructural analysis of a class I PreQ1 riboswitch aptamer in the metabolite-bound state
ComponentsPREQ1 RIBOSWITCH
KeywordsRNA / PREQ1 / PREQ0 / RIBOSOMAL BINDING SITE / APTAMER / METABOLITE / Pseudoknot / H-type / RIBOSWITCH
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.75 Å
AuthorsJenkins, J.L. / Krucinska, J. / Wedekind, J.E.
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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: PREQ1 RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1636
Polymers10,5991
Non-polymers5635
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.782, 110.782, 59.605
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-104-

SO4

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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 class I, Type 1 PreQ1 riboswitch aptamer from T. Tengcongensis
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.98 Å3/Da / Density % sol: 75.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.8 M Li2SO4, 0.05 M MES pH 5.6, and 0.01 M MgCl2(H20)6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2009 / Details: Rh coated Si vertical focus mirror
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 2.725→25 Å / Num. obs: 6041 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.85.10.586194.8
2.8-2.855.50.602199.3
2.85-2.96.10.452199
2.9-2.966.10.3591100
2.96-3.036.40.2321100
3.03-3.16.70.1871100
3.1-3.176.70.1351100
3.17-3.2670.1141100
3.26-3.366.80.102199.3
3.36-3.466.90.0911100
3.46-3.596.80.097199.3
3.59-3.736.80.086199.4
3.73-3.96.90.093199.7
3.9-4.16.80.082199
4.1-4.366.80.083198.7
4.36-4.696.70.071198.7
4.69-5.166.60.073199.3
5.16-5.96.50.06198.8
5.9-7.46.30.055198.8
7.4-255.80.041191.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6_289phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3GCA

3gca


Resolution: 2.75→22.01 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.35 / σ(F): 0.13 / Phase error: 23.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 573 10.03 %
Rwork0.2104 --
obs0.2144 5712 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.544 Å2 / ksol: 0.247 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.6181 Å2-0 Å2-0 Å2
2--12.6181 Å20 Å2
3----25.2362 Å2
Refine analyzeLuzzati sigma a obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.75→22.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 702 33 1 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007816
X-RAY DIFFRACTIONf_angle_d1.6891267
X-RAY DIFFRACTIONf_dihedral_angle_d17.512394
X-RAY DIFFRACTIONf_chiral_restr0.061164
X-RAY DIFFRACTIONf_plane_restr0.00734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-3.02620.34891320.30991135X-RAY DIFFRACTION88
3.0262-3.46260.29711440.2251298X-RAY DIFFRACTION99
3.4626-4.3570.27631440.2081315X-RAY DIFFRACTION99
4.357-22.01080.1851530.16921391X-RAY DIFFRACTION98

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