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- PDB-2a0p: Crystal structure of RNA oligomer containing 4'-thioribose -

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Basic information

Entry
Database: PDB / ID: 2a0p
TitleCrystal structure of RNA oligomer containing 4'-thioribose
Components5'-R(*CP*CP*(S4C)P*CP*GP*GP*GP*G)-3'
KeywordsRNA / A-RNA / DOUBLE HELIX / RIBONUCLEIC ACID / 4'-THIO RNA
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHaeberli, P. / Berger, I. / Pallan, P.S. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine
Authors: Haeberli, P. / Berger, I. / Pallan, P.S. / Egli, M.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*CP*CP*(S4C)P*CP*GP*GP*GP*G)-3'
B: 5'-R(*CP*CP*(S4C)P*CP*GP*GP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)5,1452
Polymers5,1452
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.440, 42.440, 127.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingrhombohedral
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

21A-168-

HOH

31A-169-

HOH

41B-144-

HOH

51B-158-

HOH

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Components

#1: RNA chain 5'-R(*CP*CP*(S4C)P*CP*GP*GP*GP*G)-3'


Mass: 2572.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesis route see publication
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Cond 39 Hampton Screen I, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 128 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.95 Å / Num. obs: 3077 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 259D

259d


Resolution: 1.95→25 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.202 -
obs0.2021 3077
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 397 0 69 466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
X-RAY DIFFRACTIONx_angle_deg3.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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