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- PDB-1efo: CRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/R... -

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Basic information

Entry
Database: PDB / ID: 1efo
TitleCRYSTAL STRUCTURE OF AN ADENINE BULGE IN THE RNA CHAIN OF A DNA/RNA HYBRID, D(CTCCTCTTC)/R(GAAGAGAGAG)
Components
  • DNA (5'-D(*CP*TP*CP*CP*TP*CP*TP*TP*C)-3')
  • RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')
KeywordsDNA-RNA HYBRID / A-FORM CONFORMATION / HYBRID / ADENINE BULGE / LOOPED OUT / DNA-RNA COMPLEX
Function / homologyDNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSudarsanakumar, C. / Xiong, Y. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag).
Authors: Sudarsanakumar, C. / Xiong, Y. / Sundaralingam, M.
History
DepositionFeb 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2000Provider: 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

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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*CP*TP*CP*TP*TP*C)-3')
B: RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,9452
Polymers5,9452
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.66, 47.61, 54.04
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

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


Mass: 2617.723 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*GP*AP*G)-3')


Mass: 3327.100 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, LITHIUM CHLORIDE, SPERMINE TETRACHLORIDE, CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1SPERMINE TETRACHLORIDE11
2CACODYLATE11
3LICL11
4MPD11
5LICL12
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
2100 mM1dropLiCl
310 mMspermine tetrachloride1drop
420 mMsodium cacodylate1drop
55 %(v/v)MPD1drop
640 %1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. all: 2880 / Num. obs: 2486 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.08 / % possible all: 71.3
Reflection
*PLUS
Num. obs: 2578 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 71.3 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 2.3→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.222 237 9 %RANDOM
Rwork0.199 ---
obs0.199 2486 91.4 %-
all-2578 --
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 394 0 23 417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4

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