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- PDB-4lvz: Structure of the THF riboswitch bound to 2,6-diaminopurine -

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Basic information

Entry
Database: PDB / ID: 4lvz
TitleStructure of the THF riboswitch bound to 2,6-diaminopurine
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 / 2 / 6-diaminopurine / mRNA
Function / homology9H-PURINE-2,6-DIAMINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THF riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9992
Polymers28,8491
Non-polymers1501
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.820, 68.510, 157.890
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-6AP / 9H-PURINE-2,6-DIAMINE / 2,6-DIAMINOPURINE


Mass: 150.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
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: 1.77→41.74 Å / Num. all: 28959 / % possible obs: 98.7 % / Observed criterion σ(F): 4.4 / Observed criterion σ(I): 4.4 / Redundancy: 3.3 %
Reflection shellResolution: 1.77→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4204 / Rsym value: 0.17 / % possible all: 99.8

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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: 1.77→28.71 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 1446 5 %5% random
Rwork0.2192 ---
obs0.2211 28895 97.73 %-
all-28959 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1913 11 307 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042149
X-RAY DIFFRACTIONf_angle_d0.9193337
X-RAY DIFFRACTIONf_dihedral_angle_d11.151050
X-RAY DIFFRACTIONf_chiral_restr0.041445
X-RAY DIFFRACTIONf_plane_restr0.00890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.768-1.83120.35211440.27852728X-RAY DIFFRACTION100
1.8312-1.90450.29371450.27082763X-RAY DIFFRACTION100
1.9045-1.99120.3121440.27662733X-RAY DIFFRACTION100
1.9912-2.09610.26721460.26292772X-RAY DIFFRACTION100
2.0961-2.22740.35011470.26542804X-RAY DIFFRACTION100
2.2274-2.39930.31331450.26022744X-RAY DIFFRACTION100
2.3993-2.64060.25861480.25692810X-RAY DIFFRACTION100
2.6406-3.02230.27781480.24112817X-RAY DIFFRACTION100
3.0223-3.80640.23191450.18832749X-RAY DIFFRACTION96
3.8064-28.71330.2131340.17372529X-RAY DIFFRACTION84

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