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- PDB-255d: CRYSTAL STRUCTURE OF AN RNA DOUBLE HELIX INCORPORATING A TRACK OF... -

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Entry
Database: PDB / ID: 255d
TitleCRYSTAL STRUCTURE OF AN RNA DOUBLE HELIX INCORPORATING A TRACK OF NON-WATSON-CRICK BASE PAIRS
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*UP*CP*GP*GP*UP*CP*C)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX / MISMATCHED
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHolbrook, S.R. / Cheong, C. / Tinoco Jr, I. / Kim, S.-H.
CitationJournal: Nature / Year: 1991
Title: Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs.
Authors: Holbrook, S.R. / Cheong, C. / Tinoco Jr., I. / Kim, S.H.
History
DepositionDec 21, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 7, 1995Provider: 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(*GP*GP*AP*CP*UP*UP*CP*GP*GP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,8041
Polymers3,8041
Non-polymers00
Water84747
1
A: RNA (5'-R(*GP*GP*AP*CP*UP*UP*CP*GP*GP*UP*CP*C)-3')

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


Theoretical massNumber of molelcules
Total (without water)7,6092
Polymers7,6092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)38.280, 32.280, 36.380
Angle α, β, γ (deg.)90.00, 124.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-39-

HOH

21A-58-

HOH

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Components

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


Mass: 3804.296 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growMethod: vapor diffusion / pH: 8.5 / Details: pH 8.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3NA CITRATE11
4MGCL211
5BIS-TRIS-PROPANE11
6WATER12
7PEG 40012
8NA CITRATE12
9MGCL212
10BIS-TRIS-PROPANE12

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 2280

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 1 /
RfactorNum. reflection% reflection
obs0.164 2082 83.9 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 255 0 47 302

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