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- PDB-1jb8: The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermol... -

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Basic information

Entry
Database: PDB / ID: 1jb8
TitleThe Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation
Components
  • 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'
  • 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
KeywordsDNA/RNA / DNA/DNA intercalation / RNA/DNA hybrid / RNA/DNA polypurine tract / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHan, G.W. / Kopka, M.L. / Langs, D. / Dickerson, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of an RNADNA hybrid reveals intermolecular intercalation: Dimer formation by base-pair swapping
Authors: Han, G.W. / Kopka, M.L. / Langs, D. / Sawaya, M.R. / Dickerson, R.E.
History
DepositionJun 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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 1.5Apr 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: 5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
B: 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,2472
Polymers6,2472
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.234, 46.780, 56.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-160-

HOH

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Components

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


Mass: 3255.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA/DNA hybrid of PPT sequence of HIV
#2: DNA chain 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3'


Mass: 2991.961 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized by the solid-phase phosphoramidate method on an Eppendorf ECOSYN D300 Synthesizer.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: MPD, magnesium acetate, spermidine, Na cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2magnesium acetate11
3spermidine11
4sodium cacodylate11
Crystal grow
*PLUS
pH: 5.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
15.14 mM1reservoirMg(OAc)2
21
31
41

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→10 Å / Num. all: 18386 / Num. obs: 2814 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.053
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.78 / % possible all: 96.9

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Processing

Software
NameClassification
DENZOdata reduction
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P2(1)2(1)2(1) structure of the same sequence of RNA/DNA hybrid

Resolution: 2.38→10 Å / Isotropic thermal model: Isotropic / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 109 5 %random
Rwork0.223 ---
all0.238 2369 --
obs-2171 --
Refinement stepCycle: LAST / Resolution: 2.38→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 414 0 66 480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg0.82
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDTotal num. of bins used
2.38-2.620.483220.451X-RAY DIFFRACTION4
2.62-2.990.36270.305X-RAY DIFFRACTION4
2.99-3.730.244410.221X-RAY DIFFRACTION4
3.73-100.162190.158X-RAY DIFFRACTION4

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