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

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Basic information

Entry
Database: PDB / ID: 3slm
TitleCrystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine-5'-monophosphate
ComponentsRNA (68-MER)
KeywordsRNA / three-way junction / riboswitch / 2'-deoxy guanosine
Function / homology2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / SUCCINIC ACID / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molrep / Resolution: 2.7 Å
AuthorsPikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.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 24, 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 / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _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

Downloads & links

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Assembly

Deposited unit
A: RNA (68-MER)
B: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,17221
Polymers44,0382
Non-polymers2,13419
Water18010
1
A: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,01310
Polymers22,0191
Non-polymers9949
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,15911
Polymers22,0191
Non-polymers1,14010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.954, 66.058, 72.503
Angle α, β, γ (deg.)90.00, 117.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-7-

MG

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (68-MER)


Mass: 22018.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcribed

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Non-polymers , 5 types, 29 molecules

#2: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Details: in vitro transcribed
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.05 M Na-succinate, ~3.0 M ammonium sulfate, 0.5 mM spermine and 20 mM magnesium chloride , pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 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: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 11084 / Num. obs: 11084 / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1100 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Molrep / Resolution: 2.7→19.543 Å / SU ML: 0.77 / σ(F): 1.34 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1082 9.83 %
Rwork0.2 --
obs0.2049 11012 99.24 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.757 Å2 / ksol: 0.283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.8187 Å20 Å210.3603 Å2
2---2.2235 Å20 Å2
3---17.0422 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2908 118 10 3036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063354
X-RAY DIFFRACTIONf_angle_d0.9925214
X-RAY DIFFRACTIONf_dihedral_angle_d21.641660
X-RAY DIFFRACTIONf_chiral_restr0.062682
X-RAY DIFFRACTIONf_plane_restr0.007141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7003-2.82280.36171380.35031220X-RAY DIFFRACTION99
2.8228-2.97120.34021400.28971227X-RAY DIFFRACTION99
2.9712-3.15660.28291210.24631242X-RAY DIFFRACTION99
3.1566-3.39910.26431510.21161199X-RAY DIFFRACTION99
3.3991-3.73910.26311230.20161237X-RAY DIFFRACTION99
3.7391-4.27520.22511180.16571272X-RAY DIFFRACTION100
4.2752-5.36770.20711390.15771257X-RAY DIFFRACTION100
5.3677-19.54390.20691520.1671276X-RAY DIFFRACTION100

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