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- PDB-1da2: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO4CG): N4-METHOXYCYTOSI... -

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Basic information

Entry
Database: PDB / ID: 1da2
TitleMOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO4CG): N4-METHOXYCYTOSINE/GUANINE BASE-PAIRS IN Z-DNA
ComponentsDNA (5'-D(*CP*GP*CP*GP*(C45)P*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsVan Meervelt, L. / Moore, M.H. / Lin, P.K.T. / Brown, D.M. / Kennard, O.
CitationJournal: J.Mol.Biol. / Year: 1990
Title: Molecular and crystal structure of d(CGCGmo4CG): N4-methoxycytosine.guanine base-pairs in Z-DNA.
Authors: Van Meervelt, L. / Moore, M.H. / Lin, P.K. / Brown, D.M. / Kennard, O.
History
DepositionOct 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 / 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(*CP*GP*CP*GP*(C45)P*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*(C45)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6802
Polymers3,6802
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.170, 30.360, 43.930
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*(C45)P*G)-3')


Mass: 1840.231 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.65 Å3/Da / Density % sol: 25.28 %
Crystal growMethod: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
224 mMsodium cacodylate1drop
312 mM1dropMgCl2
44.7 mMspermine1drop
540 %MPD1reservoir
61
71
1mMoligonucleotide1drop

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Data collection

DiffractionMean temperature: 277 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 2944
Reflection
*PLUS
Rmerge(I) obs: 0.039

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.7→10 Å /
RfactorNum. reflection
obs0.181 2559
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 4 67 311
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 2559 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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