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- PDB-5mwi: Crystal structure of G(CUG)8G duplex -

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Basic information

Entry
Database: PDB / ID: 5mwi
TitleCrystal structure of G(CUG)8G duplex
ComponentsRNA G(CUG)8C duplex
KeywordsRNA / CUG repeats / duplex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsKiliszek, A. / Blaszczyk, L. / Rypniewski, W.
Funding support Poland, 2items
OrganizationGrant numberCountry
National Science CentreUMO-2011/01/B/NZ1/04429 Poland
Ministry of Science and Higher Education0450/IP1/2013/72 Poland
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Stabilization of RNA hairpins using non-nucleotide linkers and circularization.
Authors: Kiliszek, A. / Blaszczyk, L. / Kierzek, R. / Rypniewski, W.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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 G(CUG)8C duplex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4503
Polymers8,2581
Non-polymers1922
Water1,27971
1
A: RNA G(CUG)8C duplex
hetero molecules

A: RNA G(CUG)8C duplex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9006
Polymers16,5162
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3470 Å2
ΔGint-89 kcal/mol
Surface area9220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.514, 43.514, 198.101
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

21A-233-

HOH

31A-239-

HOH

41A-270-

HOH

51A-271-

HOH

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Components

#1: RNA chain RNA G(CUG)8C duplex


Mass: 8257.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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.: 71 / 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: 43.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: magnesium acetate, cacodylate and lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. obs: 11846 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 25 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21.8
Reflection shellResolution: 1.51→1.6 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1865 / CC1/2: 0.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+48 / Resolution: 1.51→37.02 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.573 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25621 593 5 %RANDOM
Rwork0.19171 ---
obs0.19488 11249 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.937 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0.65 Å2-0 Å2
2---1.3 Å2-0 Å2
3---4.2 Å2
Refinement stepCycle: 1 / Resolution: 1.51→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 544 10 71 625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.011658
X-RAY DIFFRACTIONr_bond_other_d0.0030.02271
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.311027
X-RAY DIFFRACTIONr_angle_other_deg1.9033663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02313
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02136
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0782.947657
X-RAY DIFFRACTIONr_scbond_other5.0672.94648
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9514.4461015
X-RAY DIFFRACTIONr_long_range_B_refined5.98229.906847
X-RAY DIFFRACTIONr_long_range_B_other6.01629.688820
X-RAY DIFFRACTIONr_rigid_bond_restr5.5393928
X-RAY DIFFRACTIONr_sphericity_free34.954522
X-RAY DIFFRACTIONr_sphericity_bonded21.0285914
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.546 42 -
Rwork0.382 791 -
obs--99.64 %

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