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- PDB-1zna: CONFORMATION AND DYNAMICS IN A Z-DNA TETRAMER -

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Basic information

Entry
Database: PDB / ID: 1zna
TitleCONFORMATION AND DYNAMICS IN A Z-DNA TETRAMER
ComponentsDNA (5'-D(*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsDrew, H.R. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1981
Title: Conformation and dynamics in a Z-DNA tetramer.
Authors: Drew, H.R. / Dickerson, R.E.
#1: Journal: Nature / Year: 1980
Title: High-Salt d(CpGpCpG), a Left-Handed Z DNA Double Helix
Authors: Drew, H. / Takano, T. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionJan 26, 1981Deposition site: BNL / Processing site: BNL
Revision 1.0Mar 18, 1981Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 26, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / database_2 / database_PDB_matrix / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _symmetry.space_group_name_H-M
Details: Coordinates and structure factor indices updated from space group #20 setting B 2 21 2 to more widely recognized setting C 2 2 21
Provider: repository / Type: Remediation
Revision 3.0May 22, 2024Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.occupancy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,3842
Polymers2,3842
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.500, 31.270, 64.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-44-

HOH

21A-62-

HOH

31B-45-

HOH

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Components

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


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.96 Å3/Da / Density meas: 1.6 Mg/m3 / Density % sol: 37.33 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Crystal-IDChemical formula
10.5-1.0 M1MgCl2
21
31

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Data collection

ReflectionHighest resolution: 1.5 Å
Reflection
*PLUS
Highest resolution: 1.5 Å

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Processing

SoftwareName: JACK-LEVITT / Classification: refinement
RefinementResolution: 1.5→5.5 Å / σ(F): 2 /
RfactorNum. reflection
obs0.21 1900
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.5→5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 158 0 84 242
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 5.5 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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