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- PDB-157d: CRYSTAL AND MOLECULAR STRUCTURE OF R(CGCGAAUUAGCG): AN RNA DUPLEX... -

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Basic information

Entry
Database: PDB / ID: 157d
TitleCRYSTAL AND MOLECULAR STRUCTURE OF R(CGCGAAUUAGCG): AN RNA DUPLEX CONTAINING TWO G(ANTI).A(ANTI) BASE-PAIRS
ComponentsRNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX / MISMATCHED
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLeonard, G.A. / McAuley-Hecht, K.E. / Ebel, S. / Lough, D.M. / Brown, T. / Hunter, W.N.
CitationJournal: Structure / Year: 1994
Title: Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti).A(anti) base pairs.
Authors: Leonard, G.A. / McAuley-Hecht, K.E. / Ebel, S. / Lough, D.M. / Brown, T. / Hunter, W.N.
History
DepositionFeb 1, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3')
B: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,7032
Polymers7,7032
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.690, 34.620, 32.130
Angle α, β, γ (deg.)90.00, 127.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3851.360 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.38 Å3/Da / Density % sol: 48.43 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6MPD12

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 3863 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.057

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.8→7 Å / σ(F): 3 /
RfactorNum. reflection
obs0.19 3147
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 510 0 97 607
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 7 Å / σ(F): 3 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_chiral_restr / Dev ideal: 0.279

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