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- PDB-351d: X-RAY CRYSTAL STRUCTURES OF THE HEXAMER DCACGCG: CRYSTALS GROWN I... -

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Basic information

Entry
Database: PDB / ID: 351d
TitleX-RAY CRYSTAL STRUCTURES OF THE HEXAMER DCACGCG: CRYSTALS GROWN IN THE PRESENCE OF RUTHENIUM (II) HEXAMMINE CHLORIDE
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: 1.64 Å
AuthorsKarthe, P. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of d(CACGCG).d(CGCGTG) in crystals grown in the presence of ruthenium III hexammine chloride.
Authors: Karthe, P. / Gautham, N.
History
DepositionAug 30, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 30, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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

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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
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.880, 30.870, 44.830
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: isolated from a genetically manipulated source
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')


Mass: 1825.216 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.71 Å3/Da / Density % sol: 28.03 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2[RU(NH3)6]CL311
Crystal grow
*PLUS
pH: 6.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMhexamer duplex1drop
250 mMsodium cacodylate1drop
31 mMspermine1drop
41 mM1drop[Ru(NH3)6]Cl3
550 %MPD1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.64 Å / Num. obs: 3314

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.64→5 Å / σ(F): 2 /
RfactorNum. reflection
obs0.193 2014
Refinement stepCycle: LAST / Resolution: 1.64→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 0 37 277
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_it411
X-RAY DIFFRACTIONn_sugar_angle_it612
X-RAY DIFFRACTIONn_phos_bond_it813
X-RAY DIFFRACTIONn_phos_angle_it1014
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.020.02
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.050.04
X-RAY DIFFRACTIONn_phos_bond_d0.1060.04
X-RAY DIFFRACTIONn_phos_bond_angle_d0.060.04
X-RAY DIFFRACTIONn_plane_restr0.020.02
X-RAY DIFFRACTIONn_chiral_restr0.0840.03
X-RAY DIFFRACTIONn_singtor_nbd0.1350.063
X-RAY DIFFRACTIONn_multtor_nbd0.2770.063
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.64 Å / Lowest resolution: 5 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeight
X-RAY DIFFRACTIONn_bond_d150
X-RAY DIFFRACTIONn_angle_d150
X-RAY DIFFRACTIONn_plane_restr250
X-RAY DIFFRACTIONn_chiral_restr83.33

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