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- PDB-3ges: Crystal structure of the guanine riboswitch C74U mutant bound to ... -

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Basic information

Entry
Database: PDB / ID: 3ges
TitleCrystal structure of the guanine riboswitch C74U mutant bound to 6-O-methylguanine
ComponentsGuanine riboswitch
KeywordsRNA / riboswitch / mRNA / guanine / RNA-ligand complex / double helix / three-way junction / base triple
Function / homology6-O-methylguanine / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGilbert, S.D. / 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
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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

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Assembly

Deposited unit
A: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,02111
Polymers21,5081
Non-polymers1,51310
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.940, 35.040, 42.190
Angle α, β, γ (deg.)90.00, 89.61, 90.00
Int Tables number5
Space group name H-MC121
DetailsCoordinates for a complete multimer representing the known biologically significant monomeric state of the molecule are given.

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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-6GO / 6-O-methylguanine / 6-methoxy-7H-purin-2-amine


Mass: 165.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5O
#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.: 8 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 3K, 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
1ammonium acetate11
2PEG 3K11
3cobalt hexammine11
4K+ HEPES11
5ammonium acetate12
6PEG 3K12
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 / Detector: IMAGE PLATE / Date: Aug 23, 2005
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→19.44 Å / Num. obs: 9699 / % possible obs: 90.9 % / Observed criterion σ(I): 3 / Redundancy: 6.67 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.096 / Net I/σ(I): 11.6
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.67 % / Mean I/σ(I) obs: 3 / Num. unique all: 978 / Rsym value: 0.357 / % possible all: 91.4

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Processing

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

1u8d
PDB Unreleased entry


Resolution: 2.15→19.44 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 790331.13 / 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
Rfree0.283 514 5.3 %RANDOM
Rwork0.238 ---
obs0.238 9692 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5171 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å20 Å2-3.92 Å2
2---6.01 Å20 Å2
3---3.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.15→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 72 110 1604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.47
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: 2.15→2.28 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 92 5.7 %
Rwork0.321 1529 -
obs--91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramwater_rep.top
X-RAY DIFFRACTION2dna-rna_rep_revise.paramdna-rna_rep_revise.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cohex_rep.paramcohex_rep.top
X-RAY DIFFRACTION5OMG.paramOMG.top

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