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- PDB-181d: SEQUENCE-DEPENDENT MICROHETEROGENEITY OF Z-DNA: THE CRYSTAL AND M... -

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Basic information

Entry
Database: PDB / ID: 181d
TitleSEQUENCE-DEPENDENT MICROHETEROGENEITY OF Z-DNA: THE CRYSTAL AND MOLECULAR STRUCTURES OF D(CACGCG).D(CGCGTG) AND D(CGCACG).D(CGTGCG)
Components
  • DNA (5'-D(*CP*AP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsSadasivan, C. / Gautham, N.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Sequence-dependent microheterogeneity of Z-DNA: the crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG).
Authors: Sadasivan, C. / Gautham, N.
#1: Journal: To be Published
Title: Plasticity of Z-DNA as Observed in the Crystal Structures of Non-Selfcomplementary Hexanucleotides
Authors: Sadasivan, C. / Gautham, N.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Space Group Degeneracy in the Packing of a Non-Selfcomplementary Z-DNA Hexamer
Authors: Sadasivan, C. / Karthe, P. / Gautham, N.
History
DepositionJul 22, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 19, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 7, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.760, 30.960, 44.750
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*AP*CP*GP*CP*G)-3')


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.7 Å3/Da / Density % sol: 27.63 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.9 / Details: pH 6.90, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMduplex DNA1drop
250 mMsodium cacodylate1drop
324 mMmagnesium chloride1drop
40.1 mMspermine1drop
545 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 296 K
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. obs: 3912
Reflection
*PLUS
Highest resolution: 1.6 Å

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.6→8 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.199 2625 75 %
Refine Biso
ClassRefine-ID
ALL ATOMSX-RAY DIFFRACTION
ALL WATERSX-RAY DIFFRACTION
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 42 282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it8.194
X-RAY DIFFRACTIONn_sugar_angle_it9.46
X-RAY DIFFRACTIONn_phos_bond_it11.028
X-RAY DIFFRACTIONn_phos_angle_it11.8310
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0140.02
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0410.04
X-RAY DIFFRACTIONn_phos_bond_d0.1270.07
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0760.07
X-RAY DIFFRACTIONn_plane_restr0.0060.02
X-RAY DIFFRACTIONn_chiral_restr0.0340.03
X-RAY DIFFRACTIONn_singtor_nbd0.1180.063
X-RAY DIFFRACTIONn_multtor_nbd0.1850.063
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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