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- PDB-1vtv: Molecular structure of (M5DC-DG)3: The role of the methyl group o... -

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Basic information

Entry
Database: PDB / ID: 1vtv
TitleMolecular structure of (M5DC-DG)3: The role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA
ComponentsDNA (5'-D(*(CH3)CP*GP*(CH3)CP*GP*(CH3)CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.3 Å
AuthorsFujii, S. / Wang, A.H.-J. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A.
CitationJournal: Nucleic Acids Res. / Year: 1982
Title: Molecular Structure of (m5dC-dG)3: The Role of the Methyl Group on 5-Methyl Cytosine in Stabilizing Z-DNA
Authors: Fujii, S. / Wang, A.H.-J. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A.
History
DepositionJan 10, 1989Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: DNA (5'-D(*(CH3)CP*GP*(CH3)CP*GP*(CH3)CP*G)-3')
B: DNA (5'-D(*(CH3)CP*GP*(CH3)CP*GP*(CH3)CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,7052
Polymers3,7052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.760, 30.570, 45.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THESE PHOSPHATES ARE DISORDERED.

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Components

#1: DNA chain DNA (5'-D(*(CH3)CP*GP*(CH3)CP*GP*(CH3)CP*G)-3')


Mass: 1852.286 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.66 Å3/Da / Density % sol: 26.09 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38NA CACODYLATE1917
411SPERMINE_HCL112110
514MGCL2115113
617WATER118216
720MPD121219

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Data collection

DiffractionMean temperature: 265 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.3 Å / Num. obs: 4208 / Observed criterion σ(I): 1.5

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.3 Å / σ(I): 1.5 /
RfactorNum. reflection
obs0.156 4208
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 246 0 0 246

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