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- PDB-4xw0: Crystal structure of (GCCU(G-LNA)CCUGC)2 duplex -

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Basic information

Entry
Database: PDB / ID: 4xw0
TitleCrystal structure of (GCCU(G-LNA)CCUGC)2 duplex
ComponentsRNA (5'-R(*GP*CP*CP*UP*(LCG)P*CP*CP*UP*GP*C)-3')
KeywordsRNA / CCUG repeats / RNA duplex / Myotonic Dystrophy type 2 / tautomery / LNA residue / 3' overhanging nucleotides
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKiliszek, A. / Banaszak, K. / Rypniewski, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science CentreUMO-2011/01/B/NZ1/04429 Poland
CitationJournal: Rna / Year: 2016
Title: Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation.
Authors: Rypniewski, W. / Banaszak, K. / Kulinski, T. / Kiliszek, A.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,4744
Polymers6,2822
Non-polymers1922
Water39622
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-24 kcal/mol
Surface area3790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.910, 26.910, 80.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 3140.910 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligomer / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 40 mM magnesium sulphate, HEPES and 1.3 M lithium sulphate
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.81→27 Å / Num. obs: 5249 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.66
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1.96 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLP

3glp


Resolution: 1.81→26.91 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 524 10 %Random selection
Rwork0.2237 ---
obs0.2298 5239 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.3 Å2
Refinement stepCycle: LAST / Resolution: 1.81→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 397 10 22 429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007478
X-RAY DIFFRACTIONf_angle_d1.497743
X-RAY DIFFRACTIONf_dihedral_angle_d13.957224
X-RAY DIFFRACTIONf_chiral_restr0.05196
X-RAY DIFFRACTIONf_plane_restr0.00820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8066-1.98820.37121290.34951156X-RAY DIFFRACTION89
1.9882-2.27550.31891310.29621181X-RAY DIFFRACTION90
2.2755-2.86530.37861310.29811183X-RAY DIFFRACTION90
2.8653-190.25661330.17291189X-RAY DIFFRACTION89

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