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- PDB-472d: STRUCTURE OF AN OCTAMER RNA WITH TANDEM GG/UU MISPAIRS -

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Basic information

Entry
Database: PDB / ID: 472d
TitleSTRUCTURE OF AN OCTAMER RNA WITH TANDEM GG/UU MISPAIRS
Components
  • RNA (5'-R(*GP*UP*AP*GP*GP*CP*AP*C)-3')
  • RNA (5'-R(*GP*UP*GP*UP*UP*UP*AP*C)-3')
KeywordsRNA / GG/UU MISPAIRS / RIBONUCLEIC ACID
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDeng, J. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs.
Authors: Deng, J. / Sundaralingam, M.
History
DepositionMay 14, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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(*GP*UP*GP*UP*UP*UP*AP*C)-3')
B: RNA (5'-R(*GP*UP*AP*GP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0702
Polymers5,0702
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.920, 41.920, 56.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-32-

HOH

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Components

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


Mass: 2504.505 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*UP*AP*GP*GP*CP*AP*C)-3')


Mass: 2565.601 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 2 MM RNA (SINGLE STRAND), 0.04 M NA CACODYLATE (PH 7.0), 5% MPD, 0.050 M MGCL2, 0.001 M COBALT HEXAMINE CHORIDE, 55% MPD IN RESERVOIR, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATE11
2[CO(NH3)6]CL311
3MGCL211
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mMsodium cacodylate1drop
250 mM1dropMgCl2
31.0 mMcobalt hexamine chloride1drop
45 %(v/v)1drop
555 %1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 16, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 2708 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.055
Reflection
*PLUS
Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 288 10 %RANDOM
Rwork0.198 ---
obs0.198 2708 95.5 %-
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 335 0 34 369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.39
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_bond_d / Dev ideal: 0.01

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