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- PDB-3skr: Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2... -

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Basic information

Entry
Database: PDB / ID: 3skr
TitleCrystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, cobalt Hexammine soak
ComponentsRNA (66-MER)
KeywordsRNA / three-way junction / riboswitch / deoxyguanosine
Function / homology2'-DEOXY-GUANOSINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phaser / Resolution: 3.1 Å
AuthorsPikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.
Authors: Pikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.
History
DepositionJun 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (66-MER)
B: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,81917
Polymers42,7372
Non-polymers2,08215
Water32418
1
A: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,51410
Polymers21,3681
Non-polymers1,1469
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3047
Polymers21,3681
Non-polymers9366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.530, 35.018, 110.761
Angle α, β, γ (deg.)90.00, 92.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: RNA chain RNA (66-MER)


Mass: 21368.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: In vitro transcription
#2: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4 / Details: In vitro transcription
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M Na-HEPES, pH 7.5, ~40 % (v/v) pentaerythritol propoxylate, 0.2 M KCl and 2.0 mM spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.45 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 7273 / Num. obs: 7041 / % possible obs: 96.8 % / Observed criterion σ(I): 3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.9 / Num. unique all: 701 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Phaser / Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU ML: 0.626 / Cross valid method: THROUGHOUT / ESU R Free: 0.666 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29872 663 9.6 %RANDOM
Rwork0.23557 ---
obs0.24157 6209 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2810 105 18 2933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213244
X-RAY DIFFRACTIONr_angle_refined_deg1.14535081
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021382
X-RAY DIFFRACTIONr_nbd_refined0.1860.21388
X-RAY DIFFRACTIONr_nbtor_refined0.2840.21918
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.28
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 55 -
Rwork0.322 437 -
obs--98.01 %

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