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- PDB-409d: CRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DU... -

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Basic information

Entry
Database: PDB / ID: 409d
TitleCRYSTAL STRUCTURE OF AN RNA R(CCCIUGGG) WITH THREE INDEPENDENT DUPLEXES INCORPORATING TANDEM I.U WOBBLES
ComponentsRNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
KeywordsRNA / DOUBLE HELIX / I.U WOBBLES
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPan, B. / Mitra, S.N. / Sun, L. / Hart, D. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: Crystal structure of an RNA octamer duplex r(CCCIUGGG)2 incorporating tandem I.U wobbles.
Authors: Pan, B. / Mitra, S.N. / Sun, L. / Hart, D. / Sundaralingam, M.
History
DepositionJun 26, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 13, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
B: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
C: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
D: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
E: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
F: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)15,2556
Polymers15,2556
Non-polymers00
Water46826
1
A: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
B: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,0852
Polymers5,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
D: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,0852
Polymers5,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')
F: RNA (5'-R(*CP*CP*CP*IP*UP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,0852
Polymers5,0852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.440, 43.410, 49.390
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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


Mass: 2542.562 Da / Num. of mol.: 6 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMRNA1drop
250 mMsodium cacodylate1drop
310 mMmagnesium chloride1drop
425 mMspermine tetrachloride1drop
52.4 %1drop
640 %MPD1reservoir

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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: Oct 2, 1995
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→47.91 Å / Num. all: 4187 / Num. obs: 3912 / % possible obs: 76.5 % / Observed criterion σ(I): 1 / Redundancy: 1.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2.3 / % possible all: 58
Reflection
*PLUS
Num. obs: 4156 / % possible obs: 87.4 %
Reflection shell
*PLUS
% possible obs: 61 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: R(CCCCGGGG)

Resolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.243 381 10 %
Rwork0.185 --
all0.203 --
obs0.185 3765 80.2 %
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1008 0 26 1034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na8
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na1
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
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
Num. reflection% reflection
Rfree39 10 %
Rwork311 -
obs-60.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1

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