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- PDB-4xw1: Crystal structure of (GCCU(G-LNA)CCUG)2 duplex -

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Basic information

Entry
Database: PDB / ID: 4xw1
TitleCrystal structure of (GCCU(G-LNA)CCUG)2 duplex
ComponentsRNA (5'-R(*GP*CP*CP*UP*(LCG)P*CP*CP*UP*G)-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: 2.302 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 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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
C: RNA (5'-R(*GP*CP*CP*UP*(LCG)P*CP*CP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)2,8361
Polymers2,8361
Non-polymers00
Water1448
1
C: RNA (5'-R(*GP*CP*CP*UP*(LCG)P*CP*CP*UP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)5,6712
Polymers5,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area1890 Å2
ΔGint-2 kcal/mol
Surface area3420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.031, 26.031, 80.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11C-106-

HOH

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Components

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


Mass: 2835.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM magnesium acetate, sodium cacodylate and 1.3 M Li2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 1458 / % possible obs: 97.6 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 34.9
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.55 / % possible all: 85.5

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Processing

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

3glp


Resolution: 2.302→20 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.191 1414 100 %
Rwork0.191 --
obs0.191 1414 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 187 0 8 195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007208
X-RAY DIFFRACTIONf_angle_d1.783322
X-RAY DIFFRACTIONf_dihedral_angle_d12.47399
X-RAY DIFFRACTIONf_chiral_restr0.06943
X-RAY DIFFRACTIONf_plane_restr0.019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3023-2.38460.26011100.2601110X-RAY DIFFRACTION80
2.3846-2.480.24371280.2437128X-RAY DIFFRACTION96
2.48-2.59280.25321420.2532142X-RAY DIFFRACTION99
2.5928-2.72930.30111330.3011133X-RAY DIFFRACTION99
2.7293-2.90010.28791470.2879147X-RAY DIFFRACTION99
2.9001-3.12370.27361390.2736139X-RAY DIFFRACTION99
3.1237-3.43740.19011400.1901140X-RAY DIFFRACTION97
3.4374-3.93330.18251430.1825143X-RAY DIFFRACTION100
3.9333-4.950.12621540.1262154X-RAY DIFFRACTION99
4.95-26.03270.15651780.1565178X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 7.6478 Å / Origin y: 4.2841 Å / Origin z: 4.6019 Å
111213212223313233
T0.3682 Å20.0128 Å20.019 Å2-0.4807 Å20.0308 Å2--0.4485 Å2
L0.1075 °2-0.0414 °20.0534 °2-0.0467 °2-0.0187 °2--0.0272 °2
S-0.0057 Å °0.2064 Å °0.3664 Å °0.0758 Å °-0.1573 Å °-0.1933 Å °-0.111 Å °0.4647 Å °0.0002 Å °
Refinement TLS groupSelection: all / Selection details: chain B

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