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- PDB-1osu: STRUCTURE OF THE RNA HEXAMER, R(UUCGCG), WITH A 5'-UU-OVERHANG EX... -

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Entry
Database: PDB / ID: 1osu
TitleSTRUCTURE OF THE RNA HEXAMER, R(UUCGCG), WITH A 5'-UU-OVERHANG EXHIBITING HOOGSTEEN-LIKE TRANS U-U BASE PAIRS
ComponentsRNA (5'-R(*UP*UP*CP*GP*CP*G)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX / NICKED / 5'-UU-OVERHANG / MISMATCHED
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsWahl, M.C. / Rao, S.T. / Sundaralingam, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: The structure of r(UUCGCG) has a 5'-UU-overhang exhibiting Hoogsteen-like trans U.U base pairs.
Authors: Wahl, M.C. / Rao, S.T. / Sundaralingam, M.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of an RNA Double Helix Including Uracil-Uracil Base Pairs in an Internal Loop
Authors: Baeyens, K.J. / DeBondt, H.L. / Holbrook, S.R.
History
DepositionNov 8, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 4, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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*UP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)1,8681
Polymers1,8681
Non-polymers00
Water68538
1
A: RNA (5'-R(*UP*UP*CP*GP*CP*G)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)5,6043
Polymers5,6043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z+1/21
crystal symmetry operation4_556x,-y,-z+11
Unit cell
Length a, b, c (Å)30.600, 34.000, 29.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-41-

HOH

21A-42-

HOH

31A-43-

HOH

41A-44-

HOH

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Components

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


Mass: 1868.149 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2ISOPROPANOL11
3MG2+11
4SPERMINE11
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 %MPD1reservoir
2nonamer1drop
320 mMlithium cacodylate1drop
46-10 mM1dropor Ir(NH3)Cl3Rh(NH3)Cl3

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→8 Å / Num. obs: 2991 / Observed criterion σ(F): 2
Reflection
*PLUS
% possible obs: 86.4 % / Rmerge(I) obs: 0.024

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.161 --
obs0.161 2991 86.4 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 123 0 38 161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.7
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
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg29
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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