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

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Basic information

Entry
Database: PDB / ID: 3slq
TitleCrystal structure of the 2'- Deoxyguanosine riboswitch bound to guanosine-5'-monophosphate
ComponentsRNA (68-MER)
KeywordsRNA / three-way junction / riboswitch / 2'-deoxy guanosine
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / SUCCINIC ACID / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molrep / Resolution: 2.5 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 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_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

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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)45,55512
Polymers44,0382
Non-polymers1,51710
Water362
1
A: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8847
Polymers22,0191
Non-polymers8666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6705
Polymers22,0191
Non-polymers6514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.876, 48.390, 228.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (68-MER)


Mass: 22018.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcribed RNA
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.05 M Na-succinate, ~3.0 M (NH4)2SO4, 0.5 mM spermine and 20 mM MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.1

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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 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 14173 / Num. obs: 13677 / % possible obs: 96.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 27.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 5 / Num. unique all: 1343 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Molrep / Resolution: 2.5→19.88 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 34.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2854 1362 10.04 %
Rwork0.2371 --
obs0.2419 13571 95.98 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.196 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5895 Å20 Å2-0 Å2
2--31.4568 Å2-0 Å2
3----26.8672 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2874 88 2 2964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063291
X-RAY DIFFRACTIONf_angle_d1.0585114
X-RAY DIFFRACTIONf_dihedral_angle_d24.3631645
X-RAY DIFFRACTIONf_chiral_restr0.062672
X-RAY DIFFRACTIONf_plane_restr0.007138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.58950.49391610.41711148X-RAY DIFFRACTION97
2.5895-2.69290.42811320.38421247X-RAY DIFFRACTION98
2.6929-2.81520.38551250.3581204X-RAY DIFFRACTION98
2.8152-2.96320.40261440.31921223X-RAY DIFFRACTION98
2.9632-3.14810.30451240.27631218X-RAY DIFFRACTION95
3.1481-3.39010.34061290.26371173X-RAY DIFFRACTION94
3.3901-3.72920.28221450.24641193X-RAY DIFFRACTION94
3.7292-4.26420.23131260.19341224X-RAY DIFFRACTION95
4.2642-5.3550.22361510.17641218X-RAY DIFFRACTION95
5.355-19.88020.2021250.17651361X-RAY DIFFRACTION96

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