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- PDB-3got: Guanine riboswitch C74U mutant bound to 2-fluoroadenine. -

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Basic information

Entry
Database: PDB / ID: 3got
TitleGuanine riboswitch C74U mutant bound to 2-fluoroadenine.
ComponentsGuanine riboswitch
KeywordsRNA / riboswitch / mRNA / guanine / RNA-ligand complex / double helix / base triple / three-way junction
Function / homology2-fluoroadenine / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGilbert, S.D. / Reyes, F.E. / Batey, R.T.
CitationJournal: Structure / Year: 2009
Title: Adaptive ligand binding by the purine riboswitch in the recognition of Guanine and adenine analogs
Authors: Gilbert, S.D. / Reyes, F.E. / Edwards, A.L. / Batey, R.T.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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
Revision 2.0Aug 12, 2026Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / pdbx_entry_details ...chem_comp / pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _chem_comp.formula / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,49214
Polymers21,5081
Non-polymers1,98413
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.455, 35.084, 41.891
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain Guanine riboswitch


Mass: 21507.768 Da / Num. of mol.: 1 / Mutation: C74U / Source method: obtained synthetically
Details: This sequence was engineered based on the guanine riboswitch in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis
#2: Chemical ChemComp-A2F / 2-fluoroadenine / 2-fluoro-7H-purin-6-amine


Mass: 153.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4FN5
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22.5 % PEG 2K, 560 mM ammonium acetate, 12 mM cobalt hexammine, 10 mM K+ HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2K11
2ammonium acetate11
3cobalt hexammine11
4K+ HEPES11
5PEG 2K12
6ammonium acetate12
7cobalt hexammine12
8K+ HEPES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 8, 2006
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 13662 / % possible obs: 95.6 % / Observed criterion σ(I): 3 / Redundancy: 3.58 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.059 / Net I/σ(I): 10.2
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.21 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1133 / Rsym value: 0.315

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 768357.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1020 7.5 %RANDOM
Rwork0.218 ---
obs0.218 13630 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.8257 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å24.26 Å2
2---1.81 Å20 Å2
3---0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 92 202 1716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 144 7.2 %
Rwork0.312 1858 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1cohex_rep.paramwater_rep.top
X-RAY DIFFRACTION2dna-rna_rep_revise.paramdna-rna_rep_revise.top
X-RAY DIFFRACTION32FA.paramacetate.param
X-RAY DIFFRACTION4water_rep.paramcohex_rep.top
X-RAY DIFFRACTION5acetate.param2FA.top

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