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- PDB-5nxt: Wobble base paired RNA double helix -

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Basic information

Entry
Database: PDB / ID: 5nxt
TitleWobble base paired RNA double helix
ComponentsRNA (5'-R(*UP*GP*UP*UP*CP*UP*CP*UP*AP*CP*GP*AP*AP*GP*AP*AP*CP*A)-3')
KeywordsRNA / Double helix / Wobble pairs / N1-adenine protonation
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.379 Å
AuthorsGarg, A. / Heinemann, U.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: RNA / Year: 2018
Title: A novel form of RNA double helix based on G·U and C·A+ wobble base pairing.
Authors: Garg, A. / Heinemann, U.
History
DepositionMay 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.title / _pdbx_struct_assembly.details ..._citation.title / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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
U: RNA (5'-R(*UP*GP*UP*UP*CP*UP*CP*UP*AP*CP*GP*AP*AP*GP*AP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)5,7171
Polymers5,7171
Non-polymers00
Water1,982110
1
U: RNA (5'-R(*UP*GP*UP*UP*CP*UP*CP*UP*AP*CP*GP*AP*AP*GP*AP*AP*CP*A)-3')

U: RNA (5'-R(*UP*GP*UP*UP*CP*UP*CP*UP*AP*CP*GP*AP*AP*GP*AP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)11,4352
Polymers11,4352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)44.997, 44.997, 94.205
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11U-103-

HOH

21U-159-

HOH

31U-168-

HOH

41U-179-

HOH

51U-195-

HOH

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Components

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


Mass: 5717.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PEG 6000, Lithium chloride, Citric Acid

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.379→38.97 Å / Num. obs: 12286 / % possible obs: 99.7 % / Redundancy: 10.47 % / CC1/2: 1 / Net I/σ(I): 15.08
Reflection shellResolution: 1.38→1.46 Å / Mean I/σ(I) obs: 1.5 / CC1/2: 0.69 / % possible all: 99.8

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Processing

Software
NameClassification
PHENIXrefinement
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TS0

3ts0


Resolution: 1.379→38.969 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.09
RfactorNum. reflection% reflection
Rfree0.1514 615 5.01 %
Rwork0.1296 --
obs0.1308 12272 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.91 Å2 / Biso mean: 20.5869 Å2 / Biso min: 11.25 Å2
Refinement stepCycle: final / Resolution: 1.379→38.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 378 0 110 488
Biso mean---34.39 -
Num. residues----18
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01422
X-RAY DIFFRACTIONf_angle_d1.49655
X-RAY DIFFRACTIONf_chiral_restr0.06289
X-RAY DIFFRACTIONf_plane_restr0.0218
X-RAY DIFFRACTIONf_dihedral_angle_d7.922212
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3794-1.51820.26161490.205728282977100
1.5182-1.73790.19781500.13282840299099
1.7379-2.18960.14781520.128228923044100
2.1896-38.98410.13161640.119630973261100

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