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- PDB-438d: STRUCTURE OF AN RNA DUPLEX R(GGGCGCUCC)2 WITH NON-ADJACENT G.U BA... -

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Basic information

Entry
Database: PDB / ID: 438d
TitleSTRUCTURE OF AN RNA DUPLEX R(GGGCGCUCC)2 WITH NON-ADJACENT G.U BASE PAIRS
ComponentsRNA (5'-R(*GP*GP*GP*CP*GP*CP*UP*CP*C)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX / MISMATCHED
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsShi, K. / Wahl, M.C. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: Crystal structure of an RNA duplex r(G GCGC CC)2 with non-adjacent G*U base pairs.
Authors: Shi, K. / Wahl, M. / Sundaralingam, M.
History
DepositionDec 28, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0May 12, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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(*GP*GP*GP*CP*GP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*GP*CP*GP*CP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,7262
Polymers5,7262
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.68, 45.68, 59.95
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settinghexagonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21A-203-

HOH

31A-205-

HOH

41B-202-

HOH

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Components

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


Mass: 2862.759 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMRNA1dropsingle strand
225 mMsodium cacodylate1drop
31 mM1dropCaCl2
40.5 mMspermine tetrachloride1drop
540 %MPD1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 1521 / Num. obs: 1403 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Redundancy: 37 % / Rmerge(I) obs: 0.043

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Processing

SoftwareName: X-PLOR / Version: 3.1 / Classification: refinement
RefinementResolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.24 --RANDOM
Rwork0.186 ---
obs0.186 1403 83.8 %-
all-1521 --
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 346 0 34 380
Software
*PLUS
Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.24 / Rfactor Rwork: 0.175 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg6.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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