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- PDB-6ubu: 1.60 A resolution structure of the guanine riboswitch bound to guanine -

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Basic information

Entry
Database: PDB / ID: 6ubu
Title1.60 A resolution structure of the guanine riboswitch bound to guanine
ComponentsGuanine riboswitch aptamer domain
KeywordsRNA / riboswitch aptamer guanine purine nucleobase
Function / homologyACETATE ION / GUANINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMatyjasik, M.M. / Batey, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM073850 United States
CitationJournal: Molecules / Year: 2020
Title: High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch.
Authors: Matyjasik, M.M. / Hall, S.D. / Batey, R.T.
History
DepositionSep 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: Guanine riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,96312
Polymers21,5071
Non-polymers1,45611
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.175, 35.260, 42.276
Angle α, β, γ (deg.)90.000, 90.860, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: RNA chain Guanine riboswitch aptamer domain


Mass: 21506.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mM potassium HEPES pH 7.5, 20% v/v PEG 3000 MW, 40-50 mM cobalt hexamine, 600-650 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cryostream / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 25, 2019
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.597→19.66 Å / Num. obs: 37435 / % possible obs: 83.41 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.23 Å2 / Rpim(I) all: 0.061 / Rrim(I) all: 0.131 / Rsym value: 0.131 / Χ2: 2.015 / Net I/σ(I): 13.67
Reflection shellResolution: 1.597→1.654 Å / Redundancy: 1 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.876 / Num. unique obs: 593 / CC1/2: 0.622 / Χ2: 2.382 / % possible all: 23.15

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FE5

4fe5


Resolution: 1.6→19.66 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.37
RfactorNum. reflection% reflection
Rfree0.22 3417 9.13 %
Rwork0.2004 --
obs0.2022 37435 73.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.48 Å2
Refinement stepCycle: final / Resolution: 1.6→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 72 240 1734
Biso mean--28.31 31.13 -
Num. residues----67
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511652
X-RAY DIFFRACTIONf_angle_d1.0222605
X-RAY DIFFRACTIONf_chiral_restr0.0418334
X-RAY DIFFRACTIONf_plane_restr0.007771
X-RAY DIFFRACTIONf_dihedral_angle_d12.603800

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