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- PDB-6q57: X-ray crystal structure of the tetrahydrofolate riboswitch aptame... -

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Basic information

Entry
Database: PDB / ID: 6q57
TitleX-ray crystal structure of the tetrahydrofolate riboswitch aptamer bound to 5-deazatetrahydropterin
Componentstetrahydrofolate riboswitch aptamer
KeywordsRNA / Aptamer / riboswitch
Function / homology5-deazatetrahydropterin / RNA / RNA (> 10)
Function and homology information
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.72 Å
AuthorsDunstan, M.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: To Be Published
Title: Tetrahydrofolate Riboswitches Provide Distinct Genetic Outputs to Synthetic and Natural Signals.
Authors: Vincent, H.A. / Leigh, J. / Robinson, C.J. / Dunstan, M.S. / Ferrer Rios, M.G. / Micklefield, J.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tetrahydrofolate riboswitch aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2064
Polymers28,8491
Non-polymers3573
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.863, 68.697, 157.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain tetrahydrofolate riboswitch aptamer


Mass: 28849.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Production host: Escherichia coli K-12 (bacteria)
#2: Chemical ChemComp-T0A / 5-deazatetrahydropterin


Mass: 166.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N4O
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop
Details: 6% 2,4-methyl-pentanediol, 10 mM spermine, 40 mM Na-cacodylate, pH 7.0, 80 mM NaCl and 1 mM DTT

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→51.741 Å / Num. obs: 8282 / % possible obs: 98 % / Redundancy: 6.1 % / Net I/σ(I): 6.7
Reflection shellResolution: 2.72→2.82 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2.72→51.741 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.24
RfactorNum. reflection% reflection
Rfree0.2481 395 4.77 %
Rwork0.2102 --
obs0.2123 8282 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.84 Å2 / Biso mean: 60.1665 Å2 / Biso min: 25.48 Å2
Refinement stepCycle: final / Resolution: 2.72→51.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1913 25 2 1940
Biso mean--46.71 41.3 -
Num. residues----89
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062168
X-RAY DIFFRACTIONf_angle_d0.9933376
X-RAY DIFFRACTIONf_chiral_restr0.043445
X-RAY DIFFRACTIONf_plane_restr0.00791
X-RAY DIFFRACTIONf_dihedral_angle_d13.0231075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7201-3.11370.46441140.4052534264898
3.1137-3.92270.27391260.23632600272698
3.9227-51.75020.20141550.15422753290899

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