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- PDB-1vtw: AT Base Pairs Are Less Stable than GC Base Pairs in Z-DNA: The Cr... -

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Basic information

Entry
Database: PDB / ID: 1vtw
TitleAT Base Pairs Are Less Stable than GC Base Pairs in Z-DNA: The Crystal Structure of D(M(5)CGTAM(5)CG)
ComponentsDNA (5'-D(*(CH3)CP*GP*TP*AP*(CH3)CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.2 Å
AuthorsWang, A.H.-J. / Hakoshima, T. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1984
Title: AT Base Pairs Are Less Stable than GC Base Pairs in Z-DNA: The Crystal Structure of d(m(5)CGTAm(5)CG)
Authors: Wang, A.H.-J. / Hakoshima, T. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A.
History
DepositionAug 18, 1988Deposition 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*TP*AP*(CH3)CP*G)-3')
B: DNA (5'-D(*(CH3)CP*GP*TP*AP*(CH3)CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6752
Polymers3,6752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint16 kcal/mol
Surface area2110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.910, 30.430, 44.960
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(*(CH3)CP*GP*TP*AP*(CH3)CP*G)-3')


Mass: 1837.271 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: 1.67 Å3/Da / Density % sol: 26.22 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38NA CACODYLATE1917
411MGCL2112110
514SPERMINE115113
617WATER118216
720MPD121219

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Data collection

DiffractionMean temperature: 263 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.2 Å / Num. obs: 5412 / Observed criterion σ(I): 1.5

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.2 Å / σ(I): 1.5 /
RfactorNum. reflection
obs0.16 5412
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 244 0 0 244

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