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- PDB-2g9c: Modified pyrimidines Specifically bind the purine riboswitch -

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Basic information

Entry
Database: PDB / ID: 2g9c
TitleModified pyrimidines Specifically bind the purine riboswitch
Componentsguanine riboswitch
KeywordsRNA / mRNA / riboswitch / triaminopyrimidine / RNA-ligand complex
Function / homologyPYRIMIDINE-2,4,6-TRIAMINE / ACETATE ION / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGilbert, S.D. / Mediatore, S.J. / Batey, R.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Modified pyrimidines specifically bind the purine riboswitch.
Authors: Gilbert, S.D. / Mediatore, S.J. / Batey, R.T.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)23,62515
Polymers21,5081
Non-polymers2,11814
Water6,359353
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.990, 35.100, 41.800
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer.

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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 from the xpt-pbuX gene in Bacillus subtilis
#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.: 12 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-3AY / PYRIMIDINE-2,4,6-TRIAMINE


Mass: 125.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.35 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. all: 26583 / Num. obs: 26388 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 15.9 Å2
Reflection shellResolution: 1.58→1.64 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
BOSdata collection
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 457952.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1530 7.2 %RANDOM
Rwork0.195 ---
all0.233 21383 --
obs0.231 21203 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6037 Å2 / ksol: 0.351368 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å20 Å2-1.69 Å2
2---3.36 Å20 Å2
3----0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1422 97 353 1872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.88
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: 1.7→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 273 7.9 %
Rwork0.269 3191 -
obs--98.2 %
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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