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- PDB-3gao: Crystal structure of the guanine riboswitch bound to xanthine. -

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Basic information

Entry
Database: PDB / ID: 3gao
TitleCrystal structure of the guanine riboswitch bound to xanthine.
ComponentsGuanine riboswitch
KeywordsRNA / riboswitch / guanine / xanthine / mRNA / RNA_ligand complex / three-way junction
Function / homologyACETATE ION / COBALT HEXAMMINE(III) / XANTHINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 18, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)23,83717
Polymers21,5071
Non-polymers2,33016
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.351, 35.099, 42.248
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain Guanine riboswitch


Mass: 21506.783 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This molecule contains engineered sequences based on the guanine riboswitch found in the 5'UTR of the xpt-pbuX gene in Bacillus subtilis

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Non-polymers , 5 types, 267 molecules

#2: Chemical ChemComp-XAN / XANTHINE / Xanthine


Mass: 152.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O2
#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.: 13 / Source method: obtained synthetically / Formula: CoH18N6
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM ammonium acetate, 20 % PEG 2K, 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
2PEG200011
3Cobalt hexammine11
4K+ HEPES11
5Ammonium acetate12
6PEG200012
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: Nov 29, 2004
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.5 Å / Num. obs: 14909 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.13 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.064 / Net I/σ(I): 10.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.53 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1083 / Rsym value: 0.197

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Processing

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

1u8d
PDB Unreleased entry


Resolution: 1.9→19.49 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 430955.85 / 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
Rfree0.246 1099 7.4 %RANDOM
Rwork0.21 ---
obs0.21 14873 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9893 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å2-0.57 Å2
2---4.36 Å20 Å2
3---2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 107 251 1780
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.63
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: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 143 7.2 %
Rwork0.27 1842 -
obs--78.1 %
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 DIFFRACTION5xan2.paramxan2.top

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