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- PDB-3suy: Crystal structure of THF riboswitch, unbound status -

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Basic information

Entry
Database: PDB / ID: 3suy
TitleCrystal structure of THF riboswitch, unbound status
Componentsriboswitch
KeywordsRNA / three-way junction / pseudoknot / gene regulator
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEubacterium siraeum V10Sc8a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsHuang, L. / Serganov, A. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch.
Authors: Huang, L. / Ishibe-Murakami, S. / Patel, D.J. / Serganov, A.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2Sep 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: riboswitch


Theoretical massNumber of molelcules
Total (without water)32,8371
Polymers32,8371
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: riboswitch

X: riboswitch


Theoretical massNumber of molelcules
Total (without water)65,6752
Polymers65,6752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area3820 Å2
ΔGint-27.4 kcal/mol
Surface area31840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.172, 124.172, 150.428
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain riboswitch


Mass: 32837.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA (101-MER) / Source: (synth.) Eubacterium siraeum V10Sc8a (bacteria)
Sequence detailsTHE DATABASE REFERENCE CLOSEST TO THE CRYSTALLIZED SEQUENCE IS GB 291556121 (NUCLEOTIDES RANGE: ...THE DATABASE REFERENCE CLOSEST TO THE CRYSTALLIZED SEQUENCE IS GB 291556121 (NUCLEOTIDES RANGE: 95183-95281). TO FACILITATE CRYSTALLIZATION, NONCANONICAL BASE PAIRS WERE CONVERTED TO THEIR WATSON CRICK COUNTERPARTS BY U14A, U65C, AND U85A MUTATIONS.

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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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris-HCl, pH 7.0 4.2 M Na-formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 7473 / Num. obs: 7451 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 26.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / Num. unique all: 738 / % possible all: 99.6

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Processing

Software
NameClassification
CBASSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3SUX

3sux


Resolution: 3.21→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU B: 21.152 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.487 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26906 341 4.6 %RANDOM
Rwork0.22281 ---
all0.22499 7105 --
obs0.22499 7084 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.08 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 3.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2176 0 0 2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212437
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.36133803
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021066
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1620.2828
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2760.21488
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it0.79533504
X-RAY DIFFRACTIONr_scangle_it1.5254.53803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.211→3.292 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 --
Rwork0.298 495 -
obs--98.29 %

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