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- PDB-6uc9: Guanine riboswitch bound to O6-cyclohexylmethyl guanine -

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Basic information

Entry
Database: PDB / ID: 6uc9
TitleGuanine riboswitch bound to O6-cyclohexylmethyl guanine
ComponentsGuanine riboswitch
KeywordsRNA / riboswitch aptamer guanine purine nucleobase / O6-methylcyclohexyl guanine
Function / homologyACETATE ION / 6-O-CYCLOHEXYLMETHYL GUANINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.941 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 15, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,94110
Polymers21,5071
Non-polymers1,4349
Water3,549197
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)133.468, 35.171, 41.889
Angle α, β, γ (deg.)90.00, 91.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain Guanine riboswitch


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.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CMG / 6-O-CYCLOHEXYLMETHYL GUANINE


Mass: 247.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 10 mM potassium HEPES pH 7.5, 22.6% v/v PEG 3000 MW, 35-45 mM cobalt hexamine, and 600-650 mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 20, 2019
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.941→19.86 Å / Num. obs: 14355 / % possible obs: 97.91 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.064 / Rrim(I) all: 0.171 / Rsym value: 0.158 / Χ2: 1.041 / Net I/σ(I): 11.96
Reflection shellResolution: 1.941→2.011 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.085 / Num. unique obs: 1226 / CC1/2: 0.588 / Rpim(I) all: 0.248 / Rrim(I) all: 0.513 / Rsym value: 0.445 / Χ2: 0.536 / % possible all: 85.26

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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: 1.941→19.86 Å / Cross valid method: FREE R-VALUE / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2111 2613 9.82 %
Rwork0.1869 --
obs0.1893 14355 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine analyzeLuzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.941→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 71 197 1690
LS refinement shellResolution: 1.941→1.976 Å /
RfactorNum. reflection
Rfree0.307 97
Rwork0.2626 837

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