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- PDB-3fo6: Crystal structure of guanine riboswitch bound to 6-O-methylguanine -

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Basic information

Entry
Database: PDB / ID: 3fo6
TitleCrystal structure of guanine riboswitch bound to 6-O-methylguanine
ComponentsGuanine riboswitch
KeywordsRNA / riboswitch / mRNA / guanine / 6-O-methylguanine / RNA-ligand complex / double helix / three-way junction
Function / homology6-O-methylguanine / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionDec 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,51012
Polymers21,8361
Non-polymers1,67411
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.180, 35.270, 42.120
Angle α, β, γ (deg.)90.00, 90.45, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains one biological unit

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Components

#1: RNA chain Guanine riboswitch


Mass: 21835.990 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was engineered based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis
#2: Chemical ChemComp-6GO / 6-O-methylguanine / 6-methoxy-7H-purin-2-amine / 6-O-Methylguanine


Mass: 165.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5O
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


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.: 9 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3000, 240 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 300011
2Ammonium acetate11
3Cobalt hexammine11
4Potassium HEPES11
5PEG 300012
6Ammonium acetate12
7Cobalt hexammine12
8Potassium 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: Mar 25, 2005
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 15951 / Num. obs: 14967 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.22 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.066 / Net I/σ(I): 11.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.48 % / Mean I/σ(I) obs: 2 / Rsym value: 0.323 / % possible all: 53.1

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U8D

1u8d
PDB Unreleased entry


Resolution: 1.9→19.7 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1160795.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1057 7.4 %RANDOM
Rwork0.231 ---
obs0.231 14269 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7635 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å2-1.68 Å2
2---4.51 Å20 Å2
3---0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 79 229 1730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.44
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: 1.9→2.02 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 132 7.2 %
Rwork0.354 1697 -
obs--70.9 %

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