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- PDB-1vtt: GT Wobble Base-Pairing in Z-DNA at 1.0 Angstrom Atomic Resolution... -

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Basic information

Entry
Database: PDB / ID: 1vtt
TitleGT Wobble Base-Pairing in Z-DNA at 1.0 Angstrom Atomic Resolution: The Crystal Structure of d(CGCGTG)
ComponentsDNA (5'-D(*CP*GP*CP*GP*TP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1 Å
AuthorsHo, P.S. / Frederick, C.A. / Quigley, G.J. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. / Rich, A.
CitationJournal: Embo J. / Year: 1985
Title: GT Wobble Base-Pairing in Z-DNA at 1.0 Angstrom Atomic Resolution: The Crystal Structure of d(CGCGTG)
Authors: Ho, P.S. / Frederick, C.A. / Quigley, G.J. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. / 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 / 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*GP*CP*GP*TP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6502
Polymers3,6502
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-7 kcal/mol
Surface area2340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.450, 31.630, 45.560
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*TP*G)-3')


Mass: 1825.216 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: 1.72 Å3/Da / Density % sol: 28.58 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38NA CACODYLATE1917
411MGCL2112110
514WATER115213
617MPD118216

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Data collection

DiffractionMean temperature: 288 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 10964 / % possible obs: 79 % / Observed criterion σ(I): 1

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Processing

RefinementRfactor obs: 0.195 / Highest resolution: 1 Å
Refinement stepCycle: LAST / Highest resolution: 1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 242 0 0 242

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