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- PDB-197d: ORTHORHOMBIC CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GTACGTAC). ... -

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Basic information

Entry
Database: PDB / ID: 197d
TitleORTHORHOMBIC CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GTACGTAC). COMPARISON WITH THE TETRAGONAL STRUCTURE
ComponentsDNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.19 Å
AuthorsLanglois D'Estaintot, B. / Dautant, A. / Courseille, C. / Precigoux, G.
Citation
Journal: Eur.J.Biochem. / Year: 1993
Title: Orthorhombic crystal structure of the A-DNA octamer d(GTACGTAC). Comparison with the tetragonal structure.
Authors: Langlois d'Estaintot, B. / Dautant, A. / Courseille, C. / Precigoux, G.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1990
Title: Crystal Structure Analysis of an A(DNA) Octamer d(GTACGTAC)
Authors: Courseille, C. / Dautant, A. / Hospital, M. / Langlois D'Estaintot, B. / Precigoux, G. / Molko, D. / Teoule, R.
History
DepositionNov 24, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 7, 1995Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.605, 50.824, 21.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-78-

HOH

21B-41-

HOH

31B-58-

HOH

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Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HMD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.7 mMoctanucleotide1drop
214 mMsodium cacodylate1drop
342 mM1dropMgCl2
40.8 mMspermine hydrochloride1drop
517 %1,6-hexamethylenediol1dropmass vol.
650 %MPD1reservoirby vol.
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.19 Å / Num. all: 4465

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.19→10 Å / σ(F): 4 /
RfactorNum. reflection
obs0.161 1516
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.19→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 66 388
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_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_d0.0170.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0430.05
X-RAY DIFFRACTIONn_phos_bond_d0.0580.04
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0480.05
X-RAY DIFFRACTIONn_plane_restr0.030.03
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd0.1130.062
X-RAY DIFFRACTIONn_multtor_nbd0.150.062
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.19 Å / Lowest resolution: 10 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS

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