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- PDB-3szx: Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Rev... -

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Basic information

Entry
Database: PDB / ID: 3szx
TitleCrystal Structure of the Triplet Repeat in Myotonic Dystrophy Reveals Heterogeneous 1x1 Nucleotide UU Internal Loop Conformations
ComponentsRNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
KeywordsRNA / CUG Repeat RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsKumar, A. / Park, H. / Pengfei, F. / Parkesh, R. / Guo, M. / Nettles, K.W. / Disney, M.D.
CitationJournal: Biochemistry / Year: 2011
Title: Crystal Structure of the Triplet Repeat in Myotonic Dystrophy Reveals Heterogeneous 1x1 Nucleotide UU Internal Loop Conformations
Authors: Kumar, A. / Park, H. / Fang, P. / Parkesh, R. / Guo, M. / Nettles, K.W. / Disney, M.D.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,0792
Polymers12,0792
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-17 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.505, 39.505, 155.887
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-20-

HOH

21A-24-

HOH

31A-25-

HOH

41A-26-

HOH

51A-31-

HOH

61A-37-

HOH

71A-39-

HOH

81A-41-

HOH

91B-21-

HOH

101B-25-

HOH

111B-27-

HOH

121B-28-

HOH

131B-29-

HOH

141B-30-

HOH

151B-34-

HOH

161B-35-

HOH

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Components

#1: RNA chain RNA (5'-R(P*UP*UP*GP*GP*GP*CP*CP*UP*GP*CP*UP*GP*CP*UP*GP*GP*UP*CP*C)-3')


Mass: 6039.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Polyribonucleotide
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10 mM magnesium sulfate, 50 mM sodium cacodylate, 1.8 M lithium sulfate , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97855 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 9, 2011 / Details: Rh coated flat mirror, toroidal focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.2→33.41 Å / Num. all: 4571 / Num. obs: 4571 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.76-4.74199.8
3.29-3.76199.5
2.99-3.29199.2
2.77-2.99199.6
2.61-2.77199.8
2.48-2.611100
2.37-2.481100
2.28-2.371100
2.2-2.28199.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.204→33.41 Å / SU ML: 0.32 / σ(F): 0.13 / Phase error: 35.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 428 10.25 %random
Rwork0.2223 ---
obs0.2274 4175 91.12 %-
all-4175 --
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.097 Å2 / ksol: 0.462 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.1983 Å2-0 Å20 Å2
2---5.1983 Å20 Å2
3---10.3966 Å2
Refinement stepCycle: LAST / Resolution: 2.204→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 802 0 48 850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024890
X-RAY DIFFRACTIONf_angle_d2.151382
X-RAY DIFFRACTIONf_dihedral_angle_d14.533450
X-RAY DIFFRACTIONf_chiral_restr0.087190
X-RAY DIFFRACTIONf_plane_restr0.01338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2043-2.52310.34061340.29811132X-RAY DIFFRACTION84
2.5231-3.17850.34261500.25911282X-RAY DIFFRACTION93
3.1785-33.42080.22171440.18621333X-RAY DIFFRACTION96

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