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- PDB-421d: 5'-D(*TP*TP*CP*TP*TP*(BRO)CP*TP*TP*C)-3', 5'-R(*GP*AP*AP*GP*AP*AP... -

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Basic information

Entry
Database: PDB / ID: 421d
Title5'-D(*TP*TP*CP*TP*TP*(BRO)CP*TP*TP*C)-3', 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3'
Components
  • DNA (5'-D(*TP*TP*CP*TP*TP*(CBR)P*TP*TP*C)-3')
  • RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3')
KeywordsDNA-RNA HYBRID / DNA:RNA HYBRID DUPLEX / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsXiong, Y. / Sundaralingam, M.
CitationJournal: Structure / Year: 1998
Title: Crystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)-r(GAAGAAGAA).
Authors: Xiong, Y. / Sundaralingam, M.
History
DepositionAug 16, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,6932
Polymers5,6932
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.080, 48.080, 42.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 2726.641 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3')


Mass: 2965.895 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMhybrid1dropdouble strand
20.5 mMcobalt hexamine1drop
35 mMspermine tetrachloride1drop
480 mMsodium cacodylate1droppH7.0
510 %(v/v)MPD1drop
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: Feb 15, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→24.04 Å / Num. obs: 4948 / % possible obs: 89.3 % / Observed criterion σ(I): 1 / Redundancy: 3.46 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.355 / % possible all: 77.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 24.04 Å / Observed criterion σ(I): 1 / Redundancy: 3.46 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.237 245 5 %RANDOM
Rwork0.201 ---
obs0.201 4687 88.9 %-
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 401 0 168 569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d7.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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
Xplor fileSerial no: 1 / Param file: DNA-RNA.PARAM / Topol file: DNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg7.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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