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- PDB-1dns: BASE ONLY BINDING OF SPERMINE IN THE DEEP GROOVE OF THE A-DNA OCT... -

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Basic information

Entry
Database: PDB / ID: 1dns
TitleBASE ONLY BINDING OF SPERMINE IN THE DEEP GROOVE OF THE A-DNA OCTAMER D(GTGTACAC)
ComponentsDNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsJain, S.C. / Zon, G. / Sundaralingam, M.
Citation
Journal: Biochemistry / Year: 1989
Title: Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC).
Authors: Jain, S. / Zon, G. / Sundaralingam, M.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: The Potentially Z-DNA-Forming Sequence d(GTGTACAC) Crystallizes as A-DNA
Authors: Jain, S. / Zon, G. / Sundaralingam, M.
History
DepositionFeb 22, 1989Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6292
Polymers2,4271
Non-polymers2021
Water00
1
A: DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')
hetero molecules

A: DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2584
Polymers4,8532
Non-polymers4052
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.430, 42.430, 24.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.41 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDChemical formula
1spermine1
21MgCl2
31
41
51
61

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-6
DetectorDetector: OSCILLATION CAMERA
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 1365 / Observed criterion σ(I): 3

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2→5 Å /
RfactorNum. reflection
obs0.115 1214
Refine Biso
ClassRefine-IDDetailsTreatment
ATOMS OF ONE STRANDX-RAY DIFFRACTIONTRisotropic
HALF SPERMINEX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 7 0 168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.01
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: 2 Å / Lowest resolution: 5 Å / Num. reflection obs: 1214 / Rfactor obs: 0.115
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.01
X-RAY DIFFRACTIONn_angle_deg1.7

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