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- PDB-4lvv: Structure of the THF riboswitch -

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Basic information

Entry
Database: PDB / ID: 4lvv
TitleStructure of the THF riboswitch
ComponentsTHF riboswitch
KeywordsRNA / Aptamers / Nucleotide / 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 / S-Adenosylmethionine / Streptococcus mutans / Terminator Regions / Genetic / Tetrahydrofolates / Thermodynamics / Transcription / three-way junction / pseudoknot / regulation / ncRNA / THF binding / mRNA
Function / homologyChem-FFO / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
SupersessionMar 19, 2014ID: 3SD1
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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THF riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7963
Polymers28,8491
Non-polymers9472
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.810, 67.410, 156.680
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-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N7O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
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: 2.1→52.23 Å / Num. all: 17948 / % possible obs: 99.3 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 3.2 / Redundancy: 3.8 %
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.17 / % possible all: 98

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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: 2.1→33.705 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 888 4.99 %
Rwork0.2027 --
obs0.2039 17807 98.51 %
all-17948 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→33.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1913 59 73 2045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052205
X-RAY DIFFRACTIONf_angle_d1.0473428
X-RAY DIFFRACTIONf_dihedral_angle_d12.2271092
X-RAY DIFFRACTIONf_chiral_restr0.045448
X-RAY DIFFRACTIONf_plane_restr0.00899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.23170.35531440.29252716X-RAY DIFFRACTION97
2.2317-2.40390.33261440.28582783X-RAY DIFFRACTION99
2.4039-2.64580.29931470.28082784X-RAY DIFFRACTION99
2.6458-3.02840.26721460.26632810X-RAY DIFFRACTION99
3.0284-3.81460.23771490.19032838X-RAY DIFFRACTION99
3.8146-33.70930.16321580.15362988X-RAY DIFFRACTION98

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