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- PDB-2eew: Guanine Riboswitch U47C mutant bound to hypoxanthine -

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Basic information

Entry
Database: PDB / ID: 2eew
TitleGuanine Riboswitch U47C mutant bound to hypoxanthine
ComponentsGuanine riboswitch
KeywordsRNA / riboswitch / mRNA / RNA-ligand complex / three-way junction / hypoxanthine / guanine / base triple
Function / homologyACETATE ION / HYPOXANTHINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGilbert, S.D. / Love, C.E. / Batey, R.T.
CitationJournal: Biochemistry / Year: 2007
Title: Mutational analysis of the purine riboswitch aptamer domain
Authors: Gilbert, S.D. / Love, C.E. / Edwards, A.L. / Batey, R.T.
History
DepositionFeb 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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
Remark 999SEQUENCE Residues C47 was engineered from U based on the guanine riboswitch found in the 5'UTR of ...SEQUENCE Residues C47 was engineered from U based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis.

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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)22,99011
Polymers21,5061
Non-polymers1,48410
Water4,270237
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.107, 35.258, 42.010
Angle α, β, γ (deg.)90.00, 90.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain Guanine riboswitch


Mass: 21505.801 Da / Num. of mol.: 1 / Mutation: U47C / 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.
References: PDB-PDB
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 161.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% Polyethylene glycol 3000, 720mM ammonium acetate, 10mM cobalt hexammine chloride, 10mM K(+)-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Polyethylene glycol 300011
2ammonium acetate11
3cobalt hexammine chloride11
4K(+)-Hepes11
5H2O11
6Polyethylene glycol 300012
7ammonium acetate12
8cobalt hexammine chloride12
9K(+)-Hepes12
10H2O12

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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: Jul 7, 2006 / Details: RU-200/Confocal blue optic source
RadiationMonochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→14.85 Å / Num. all: 13409 / Num. obs: 13088 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 2.68 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.057 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1331 / Rsym value: 0.225 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U8D

1u8d
PDB Unreleased entry


Resolution: 2.25→14.85 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 669000.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.285 933 10.2 %RANDOM
Rwork0.234 ---
obs0.234 9165 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-10.39 Å20 Å24.83 Å2
2---9.94 Å20 Å2
3----0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.25→14.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 70 237 1729
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_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
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: 2.25→2.33 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 147 9.6 %
Rwork0.264 1382 -
obs-1382 98.1 %
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 DIFFRACTION5acetate.paramacetate.top

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