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- PDB-413d: A'-FORM RNA DOUBLE HELIX IN THE SINGLE CRYSTAL STRUCTURE OF R(UGA... -

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Basic information

Entry
Database: PDB / ID: 413d
TitleA'-FORM RNA DOUBLE HELIX IN THE SINGLE CRYSTAL STRUCTURE OF R(UGAGCUUCGGCUC)
ComponentsRNA (5'-R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP*UP*C)-3')
KeywordsRNA / A'-RNA / DOUBLE HELIX
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTanaka, Y. / Fujii, S. / Hiroaki, H. / Sakata, T. / Tanaka, T. / Uesugi, S. / Tomita, K.-I. / Kyogoku, Y.
Citation
Journal: Nucleic Acids Res. / Year: 1999
Title: A'-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC).
Authors: Tanaka, Y. / Fujii, S. / Hiroaki, H. / Sakata, T. / Tanaka, T. / Uesugi, S. / Tomita, K. / Kyogoku, Y.
#1: Journal: Nucleic Acids Symp.Ser. / Year: 1992
Title: Conformational features of the four successive non-Watson-Crick base pairs in RNA duplex
Authors: Fujii, S. / Tanaka, Y. / Uesugi, S. / Tanaka, T. / Sakata, T. / Hiroaki, H.
#2: Journal: Nucleic Acids Symp.Ser. / Year: 1991
Title: Molecular structure of extraordinarily stable RNA : model building and X-ray analysis
Authors: Fujii, S. / Tanaka, Y. / Tomita, K.-I. / Sakata, T. / Hiroaki, H. / Tanaka, T. / Uesugi, S.
History
SupersessionJul 10, 1998ID: 373D
DepositionJul 10, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 10, 1998Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,1101
Polymers4,1101
Non-polymers00
Water66737
1
A: RNA (5'-R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP*UP*C)-3')

A: RNA (5'-R(*UP*GP*AP*GP*CP*UP*UP*CP*GP*GP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,2212
Polymers8,2212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)38.490, 32.300, 38.760
Angle α, β, γ (deg.)90.00, 117.56, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1-

U

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Components

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


Mass: 4110.461 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMRNA tridecamer1drop
26.7 mMsodium cacodylate1drop
31.3 mMsodium phosphate1drop
413.3 mM1dropNaCl
53.3 mM1dropBaCl2
63.7 mMspermine-3HCl1drop
70.8 %PEG4001drop
84 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Dec 15, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. all: 3556 / Num. obs: 3556 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
% possible obs: 90.1 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 258 9.4 %RANDOM
Rwork0.182 ---
obs0.182 2743 69.3 %-
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 288 0 37 325
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_deg0.9
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: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 2942 / Num. reflection Rfree: 318 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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