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- PDB-1d53: CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN ... -

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Basic information

Entry
Database: PDB / ID: 1d53
TitleCRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN OCTANUCLEOTIDE CONTAINING INOSINE, AND ITS COMPARISON WITH D(CGCG) AND D(CGCGCG) STRUCTURES
Components
  • DNA (5'-D(*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsKumar, V.D. / Harrison, R.W. / Andrews, L.C. / Weber, I.T.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystal structure at 1.5-A resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures.
Authors: Kumar, V.D. / Harrison, R.W. / Andrews, L.C. / Weber, I.T.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: The Molecular Structure of the Left-Handed Z-DNA Double Helix at 1.0 Angstrom Atomic Resolution. Geometry, Conformation, and Ionic Interaction of d(CGCGCG)
Authors: Gessner, R.V. / Frederick, C.A. / Quigley, G.J. / Rich, A. / Wang, A.H.-J.
#2: Journal: Biopolymers / Year: 1985
Title: The Octamers d(CGCGCGCG) and d(CGCATGCG) Both Crystallize as Z-DNA in the Same Hexagonal Lattice
Authors: Fujii, S. / Wang, A.H.-J. / Quigley, G.J. / Westerink, H. / Van Der Marel, G. / Van Boom, J.H. / Rich, A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: The Tetramer d(CpGpCpG) Crystallizes as a Left-Handed Double Helix
Authors: Crawford, J.L. / Kolpak, F.J. / Wang, A.H.-J. / Quigley, G.J. / Van Boom, J.H. / Van Der Marel, G. / Rich, A.
#4: Journal: Nature / Year: 1980
Title: High-Salt d(CpGpCpG), a Left-Handed Z'DNA Double Helix
Authors: Drew, H. / Takano, T. / Tanaka, S. / Itakura, K. / Dickerson, R.
History
DepositionNov 5, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,5304
Polymers3,5304
Non-polymers00
Water1,24369
1
A: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')

A: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')

A: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')

A: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,5878
Polymers4,5878
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x-y,x,z-1/61
crystal symmetry operation3_555-x+y,-x,z+1/31
crystal symmetry operation5_555y,-x+y,z+1/61
2
C: DNA (5'-D(*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*G)-3')

C: DNA (5'-D(*CP*GP*CP*G)-3')
D: DNA (5'-D(*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,7674
Polymers4,7674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
Unit cell
Length a, b, c (Å)31.000, 31.000, 43.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 573.430 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.72 Å3/Da / Density % sol: 28.36 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4MG ACETATE11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mMDNA oligonucleotide1drop
21 mMspermine1drop
314 mMmagnesium acetate1drop
420 %MPD1drop

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 9882 / Num. obs: 1971
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. all: 2134 / Num. measured all: 9882 / Rmerge(I) obs: 0.081

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Processing

Software
NameClassification
X-PLORrefinement
NUCLSQrefinement
RefinementResolution: 1.5→5 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.225 -
obs0.225 2503
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 234 0 69 303
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 5 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_plane_restr0.0420.03
X-RAY DIFFRACTIONx_chiral_restr0.1140.1

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