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- PDB-3rkf: Crystal structure of guanine riboswitch C61U/G37A double mutant b... -

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Basic information

Entry
Database: PDB / ID: 3rkf
TitleCrystal structure of guanine riboswitch C61U/G37A double mutant bound to thio-guanine
ComponentsGuanine riboswitch
KeywordsRNA / three-way junction / riboswitch / m-RNA / thioguanine
Function / homology2-amino-1,9-dihydro-6H-purine-6-thione / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBuck, J. / Wacker, A. / Warkentin, E. / Woehnert, J. / Wirmer-Bartoschek, J. / Schwalbe, H.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain.
Authors: Buck, J. / Wacker, A. / Warkentin, E. / Wohnert, J. / Wirmer-Bartoschek, J. / Schwalbe, H.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Sep 13, 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
B: Guanine riboswitch
C: Guanine riboswitch
D: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,95334
Polymers86,0954
Non-polymers4,85830
Water21612
1
A: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,14111
Polymers21,5241
Non-polymers1,61710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4977
Polymers21,5241
Non-polymers9736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4977
Polymers21,5241
Non-polymers9736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Guanine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8199
Polymers21,5241
Non-polymers1,2958
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.300, 52.300, 263.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: RNA chain
Guanine riboswitch


Mass: 21523.766 Da / Num. of mol.: 4 / Mutation: C61U G37A / Source method: obtained synthetically
#2: Chemical
ChemComp-DX4 / 2-amino-1,9-dihydro-6H-purine-6-thione


Mass: 167.192 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5S / Comment: medication*YM
#3: Chemical...
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5mM K+ - HEPES, 12mM [Co(NH3)6]3+, 25% polyethylene glycol 4000, 450mM ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.02 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2009
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.5→44.64 Å / Num. all: 67756 / Num. obs: 26059 / % possible obs: 93.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1u8d

1u8d
PDB Unreleased entry


Resolution: 2.5→44.638 Å / σ(F): 1.96 / Phase error: 30.98 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1156 4.45 %random
Rwork0.2073 ---
obs0.2084 25949 93.14 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.729 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8347 Å20 Å2-0 Å2
2--1.8347 Å20 Å2
3----3.6695 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5708 226 12 5946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026580
X-RAY DIFFRACTIONf_angle_d0.49210390
X-RAY DIFFRACTIONf_dihedral_angle_d16.4593204
X-RAY DIFFRACTIONf_chiral_restr0.0541340
X-RAY DIFFRACTIONf_plane_restr0.002272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5084-2.62220.40521290.38862785X-RAY DIFFRACTION81
2.6222-2.75980.47021340.45372901X-RAY DIFFRACTION84
2.7598-2.93180.31341430.30693257X-RAY DIFFRACTION96
2.9318-3.15680.3021520.24653264X-RAY DIFFRACTION95
3.1568-3.47180.24131780.23663056X-RAY DIFFRACTION88
3.4718-3.96820.27321150.21012778X-RAY DIFFRACTION81
3.9682-4.97690.181370.15983271X-RAY DIFFRACTION95
4.9769-16.56880.13791680.13473248X-RAY DIFFRACTION94

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