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- PDB-4lw0: Structure of the THF riboswitch bound to adenine -

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Basic information

Entry
Database: PDB / ID: 4lw0
TitleStructure of the THF riboswitch bound to adenine
ComponentsTHF riboswitch
KeywordsRNA / Aptamers / Nucleotide / Bacillus subtilis / Bacterial Proteins / Base Sequence / Binding Sites / Calorimetry / Folic Acid / Gene Expression Regulation / Bacterial / Guanine / Leucovorin / Ligands / Magnesium / Molecular Sequence Data / Nucleic Acid Conformation / Point Mutation / Protein Binding / Protein Structure / Secondary / Riboswitch / S-Adenosylmethionine / Streptococcus mutans / Terminator Regions / Genetic / Tetrahydrofolates / Thermodynamics / Transcription / three-way junction / pseudoknot / regulation / ncRNA / Adenine binding / mRNA
Function / homologyADENINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.889 Å
AuthorsTrausch, J.J. / Batey, R.T.
Citation
Journal: Chem.Biol. / Year: 2014
Title: A Disconnect between High-Affinity Binding and Efficient Regulation by Antifolates and Purines in the Tetrahydrofolate Riboswitch.
Authors: Trausch, J.J. / Batey, R.T.
#1: Journal: Structure / Year: 2011
Title: The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.
Authors: Trausch, J.J. / Ceres, P. / Reyes, F.E. / Batey, R.T.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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:
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Assembly

Deposited unit
A: THF riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9842
Polymers28,8491
Non-polymers1351
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.180, 68.460, 157.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain THF riboswitch


Mass: 28849.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 in vitro transcribed
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2,4-methyl-pentanediol, spermine, sodium cacodylate, sodium chloride, dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1051 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1051 Å / Relative weight: 1
ReflectionResolution: 1.75→41.86 Å / Num. all: 26159 / % possible obs: 85.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.3 %
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3 / Rsym value: 0.265 / % possible all: 75.5

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.889→34.23 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 1206 5.01 %
Rwork0.2056 --
obs0.2068 24074 98.13 %
all-26159 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.889→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1913 10 165 2088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042153
X-RAY DIFFRACTIONf_angle_d0.9653355
X-RAY DIFFRACTIONf_dihedral_angle_d12.0071065
X-RAY DIFFRACTIONf_chiral_restr0.042445
X-RAY DIFFRACTIONf_plane_restr0.00790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8891-1.96480.33041210.32122262X-RAY DIFFRACTION89
1.9648-2.05420.2971330.2732502X-RAY DIFFRACTION99
2.0542-2.16240.31571300.26432497X-RAY DIFFRACTION99
2.1624-2.29790.2631340.26742550X-RAY DIFFRACTION99
2.2979-2.47530.311350.26462555X-RAY DIFFRACTION100
2.4753-2.72430.27481350.26542584X-RAY DIFFRACTION100
2.7243-3.11830.25441360.23912557X-RAY DIFFRACTION100
3.1183-3.92780.21621370.1762618X-RAY DIFFRACTION99
3.9278-34.23560.16431450.15242743X-RAY DIFFRACTION99

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