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- PDB-239d: POLYMORPHISM IN LEFT HANDED DNA: THE CRYSTAL STRUCTURE OF D(CCCGGG)2 -

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Basic information

Entry
Database: PDB / ID: 239d
TitlePOLYMORPHISM IN LEFT HANDED DNA: THE CRYSTAL STRUCTURE OF D(CCCGGG)2
ComponentsDNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsKarthe, P. / Krishnaswamy, S. / Gautham, N.
CitationJournal: To be Published / Year: 1996
Title: Polymorphism in Left Handed DNA: The Crystal Structure of d(CCCGGG)2
Authors: Karthe, P. / Krishnaswamy, S. / Gautham, N.
History
DepositionNov 2, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 14, 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*CP*CP*GP*GP*G)-3')
B: DNA (5'-D(*CP*CP*CP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.764, 30.925, 43.922
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*CP*CP*GP*GP*G)-3')


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.67 Å3/Da / Density % sol: 26.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.98
Details: pH 6.98, VAPOR DIFFUSION, HANGING DROP, temperature 296.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2BACL211
3SPERMINE11
4NA CACODYLATE11
5WATER12
6MPD12

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Data collection

DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. all: 1727 / Num. obs: 1704 / % possible obs: 44 %

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Processing

Software
NameClassification
X-PLORrefinement
NUCLSQrefinement
RefinementResolution: 2.05→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.352 -
Rwork0.212 -
obs0.212 733
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.05→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 31 271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.03
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_deg5.7
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

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