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- PDB-404d: CRYSTAL STRUCTURE OF THE RNA/DNA HYBRID R(GAAGAGAAGC). D(GCTTCTCTTC) -

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Basic information

Entry
Database: PDB / ID: 404d
TitleCRYSTAL STRUCTURE OF THE RNA/DNA HYBRID R(GAAGAGAAGC). D(GCTTCTCTTC)
Components
  • 5'-D(*GP*CP*TP*TP*CP*TP*CP*TP*TP*C)-3'
  • 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'
KeywordsDNA-RNA HYBRID / RNA/DNA HYBRID R(GAAGAGAAGC).D(GCTTCTCTTC) / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsConn, G. / Brown, T. / Leonard, G.A.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) shows significant differences to that found in solution.
Authors: Conn, G.L. / Brown, T. / Leonard, G.A.
History
DepositionJun 12, 1998Deposition site: NDB / Processing site: RCSB
Revision 1.0Dec 14, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.4Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'
B: 5'-D(*GP*CP*TP*TP*CP*TP*CP*TP*TP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,2492
Polymers6,2492
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.720, 45.550, 47.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3287.076 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*TP*TP*CP*TP*CP*TP*TP*C)-3'


Mass: 2961.940 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2PEG400011
3AMMONIUM ACETATE11
4MGCL211
5HEPES12
6PEG400012
7AMMONIUM ACETATE12
8MGCL212
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mM1reservoir
25 %1reservoir
3200 mMammonium acetate1reservoir
4150 mMmagnesium acetate1reservoir
51
61
71
81

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: PRINCETON 2K / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 1881 / Num. obs: 1881 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.06 % / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementResolution: 2.5→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rwork0.184 --
all0.181 1867 -
obs0.181 1867 86.6 %
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 414 0 9 423
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d0.047

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