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- PDB-1d80: CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BAS... -

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Basic information

Entry
Database: PDB / ID: 1d80
TitleCRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*GP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MISMATCHED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsSkelly, J.V. / Edwards, K.J. / Jenkins, T.C. / Neidle, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation.
Authors: Skelly, J.V. / Edwards, K.J. / Jenkins, T.C. / Neidle, S.
History
DepositionJun 17, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,4072
Polymers7,4072
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.440, 41.580, 66.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*GP*GP*CP*G)-3')


Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 279 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 279.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SPERMINE11
3MGCL211
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 279 K / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 mMspermine1drop
21.3 mMDNA1drop
316 mM1dropMgCl2
430 mMsodium cacodylate1drop
528 %(v/v)MPD1reservoir
61

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 8732 / Num. obs: 3811
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. measured all: 14624

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(I): 2 /
RfactorNum. reflection
obs0.188 2365
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 0 72 564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it4.15
X-RAY DIFFRACTIONn_sugar_angle_it5.77.5
X-RAY DIFFRACTIONn_phos_bond_it5.7897.5
X-RAY DIFFRACTIONn_phos_angle_it6.60210
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0130.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0310.04
X-RAY DIFFRACTIONn_phos_bond_d0.0580.05
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0680.075
X-RAY DIFFRACTIONn_plane_restr0.0190.03
X-RAY DIFFRACTIONn_chiral_restr0.0720.1
X-RAY DIFFRACTIONn_singtor_nbd0.1870.25
X-RAY DIFFRACTIONn_multtor_nbd0.2350.25
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(I): 2 / Num. reflection obs: 2365 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_mcbond_it5.7897.5
X-RAY DIFFRACTIONn_mcangle_it6.60210

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