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- PDB-3g4m: Crystal structure of guanine riboswitch bound to 2-aminopurine -

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Basic information

Entry
Database: PDB / ID: 3g4m
TitleCrystal structure of guanine riboswitch bound to 2-aminopurine
ComponentsGuanine riboswitch
KeywordsRNA / riboswitch / mRNA / 2-aminopurine / guanine / three-way junction / RNA-ligand complex / double helix / base-triple.
Function / homology9H-purin-2-amine / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 4, 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)23,47314
Polymers21,5071
Non-polymers1,96613
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.430, 35.160, 42.240
Angle α, β, γ (deg.)90.00, 91.18, 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
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-2BP / 9H-purin-2-amine / 2-AMINOPURINE / 2-Aminopurine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#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.: 11 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3K, 12.5 mM cobalt hexammine, 600mM ammonium acetate, 10 mM K-HEPES., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 300011
2Cobalt hexammine11
3Ammonium acetate11
4K-HEPES11
5PEG 300012
6Cobalt hexammine12
7Ammonium acetate12
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: Nov 17, 2008
RadiationMonochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→19.92 Å / Num. obs: 13481 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 1.83 % / Rsym value: 0.08 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.64 % / Mean I/σ(I) obs: 3 / Rsym value: 0.284 / % possible all: 86

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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: 1U8D

1u8d
PDB Unreleased entry


Resolution: 2.4→19.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 320880.12 / 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
Rfree0.278 1296 9.7 %RANDOM
Rwork0.229 ---
obs0.229 13374 93.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.0612 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.97 Å20 Å28.8 Å2
2---11.53 Å20 Å2
3---4.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 91 64 1577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
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_deg0.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
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: 2.4→2.55 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 188 9.1 %
Rwork0.382 1876 -
obs--86.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep_revise.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4cohex_rep.paramcohex_rep.top
X-RAY DIFFRACTION5hpa5.paramhpa5.top

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