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- PDB-479d: CRYSTAL STRUCTURE A DNA:RNA HYBRID DUPLEX, A DYNAMIC MODEL FOR RN... -

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Basic information

Entry
Database: PDB / ID: 479d
TitleCRYSTAL STRUCTURE A DNA:RNA HYBRID DUPLEX, A DYNAMIC MODEL FOR RNASE H RECOGNITION
Components
  • DNA (5'-D(*CP*TP*CP*TP*TP*CP*TP*TP*C)-3')
  • RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
KeywordsDNA-RNA HYBRID / A-T-RNA / DOUBLE HELIX / DNA/RNA HYBRID / DNA-RNA HYBRID complex
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsXiong, Y. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC).
Authors: Xiong, Y. / Sundaralingam, M.
History
DepositionJul 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Structure summary / Category: software / struct_keywords / Item: _struct_keywords.text
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: DNA (5'-D(*CP*TP*CP*TP*TP*CP*TP*TP*C)-3')
B: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,6152
Polymers5,6152
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.15, 49.15, 46.13
Angle α, β, γ (deg.)90.0, 90.0, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

#1: DNA chain DNA (5'-D(*CP*TP*CP*TP*TP*CP*TP*TP*C)-3')


Mass: 2632.734 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Mass: 2981.895 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: DROP: 1 MM HYBID (DOUBLE STRAND), 400 MM MGCL2, 0.10 M SODIUM CACODYLATE (PH 6.0), 2MM SPERMINE TETRACHLORIDE, 5% MPD; RESERVOIR: 40 % MPD, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SODIUM CACODYLATE11
3SPERMINE TETRACHLORIDE11
4MPD11
5MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
2400 mM1dropMgCl2
32 mMspermine tetrachloride1drop
4100 mMsodium cacodylate1drop
55 %(v/v)1drop
640 %MPD1reservoir

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 15, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→31.38 Å / Num. obs: 4443 / % possible obs: 87.9 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 5382 / % possible obs: 91 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.9→10 Å / Cross valid method: LUZZATI PLOT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.262 208 5 %
Rwork0.199 --
obs0.199 4373 87.84 %
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 372 0 37 409
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
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_deg0.008
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
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.179 / Rfactor Rfree: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.26
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg8.08

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