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- PDB-212d: INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAME... -

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Basic information

Entry
Database: PDB / ID: 212d
TitleINFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAMERS: BINDING OF [CO(NH3)6]3+ AND BA2+ TO A-DNA
ComponentsDNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyCOBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsGao, Y.-G. / Robinson, H. / Van Boom, J.H. / Wang, A.H.-J.
CitationJournal: Biophys.J. / Year: 1995
Title: Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA.
Authors: Gao, Y.G. / Robinson, H. / van Boom, J.H. / Wang, A.H.
History
DepositionJun 26, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 31, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5294
Polymers3,0461
Non-polymers4833
Water1,18966
1
A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
hetero molecules

A: DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')
hetero molecules


  • defined by author
  • 7.06 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)7,0598
Polymers6,0922
Non-polymers9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)39.092, 39.092, 77.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*GP*GP*CP*CP*GP*GP*T)-3')


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growMethod: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4[CO(NH3)6]3+11
5WATER13
6[CO(NH3)6]3+13
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDDetails
14 mMDNA duplex10.0025 ml
250 mMsodium cacodylate10.01 ml
320 %MPD10.0025 ml
410 mM10.0025 ml
51
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 2163
Reflection
*PLUS
Rmerge(I) obs: 0.066

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.9 Å / σ(F): 4 /
RfactorNum. reflection
obs0.194 2163
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 21 66 289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.021
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.021

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