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- PDB-1dn6: THE CRYSTAL STRUCTURE OF D(GGATGGGAG). AN ESSENTIAL PART OF THE B... -

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Basic information

Entry
Database: PDB / ID: 1dn6
TitleTHE CRYSTAL STRUCTURE OF D(GGATGGGAG). AN ESSENTIAL PART OF THE BINDING SITE FOR TRANSCRIPTION FACTOR IIIA
Components
  • DNA (5'-D(*CP*TP*CP*CP*CP*AP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*TP*GP*GP*GP*AP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsMcCall, M. / Brown, T. / Hunter, W.N. / Kennard, O.
CitationJournal: Nature / Year: 1986
Title: The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA.
Authors: McCall, M. / Brown, T. / Hunter, W.N. / Kennard, O.
History
DepositionMay 11, 1987Deposition site: BNL / Processing site: BNL
Revision 1.0Jan 16, 1988Provider: 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 / 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(*GP*GP*AP*TP*GP*GP*GP*AP*G)-3')
B: DNA (5'-D(*CP*TP*CP*CP*CP*AP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,4732
Polymers5,4732
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.290, 45.290, 24.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 2860.884 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*TP*CP*CP*CP*AP*TP*CP*C)-3')


Mass: 2611.726 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4NA CACODYLATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-20 %MPD1reservoir
20.2 mMDNA1drop
312 mMmagnesium acetate1drop
412 mMsodium cacodylate1drop
50.8 mMspermine HCl1drop
61
71

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Data collection

DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 1786 / Num. obs: 1459
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 3 Å / Observed criterion σ(I): 1 / Num. measured all: 1786
Reflection shell
*PLUS

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 3→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.33 1032
Refine Biso Class: ALL ATOMS / Details: TF / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 363 0 0 363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.022
X-RAY DIFFRACTIONn_angle_d0.054
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: 3 Å / Lowest resolution: 10 Å / Num. reflection all: 1032 / Rfactor all: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.022
X-RAY DIFFRACTIONn_angle_d0.054

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