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- PDB-309d: A DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT -

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Basic information

Entry
Database: PDB / ID: 309d
TitleA DNA DECAMER WITH A STICKY END: THE CRYSTAL STRUCTURE OF D-CGACGATCGT
ComponentsDNA (5'-D(*CP*GP*AP*CP*GP*AP*TP*CP*GP*T)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / OVERHANGING BASES / CONTINUOUS HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsQiu, H.X. / Dewan, J.C. / Seeman, N.C.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT.
Authors: Qiu, H. / Dewan, J.C. / Seeman, N.C.
History
DepositionJan 7, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Jan 22, 1997Provider: repository / Type: Initial release
SupersessionFeb 12, 1997ID: 273D
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Data collection / Experimental preparation / Category: diffrn / exptl_crystal_grow
Item: _diffrn.ambient_temp / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.450, 34.660, 32.170
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3045.004 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMDNA1drop
230 mMmagnesium acetate1drop
31 Mspermine1drop
410 %(v/v)MPD1drop
515 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. obs: 1768 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→3.6 Å / % possible all: 75

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.214 1421
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 68 472
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_d0.010.02
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0230.03
X-RAY DIFFRACTIONn_phos_bond_d0.0230.03
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0310.04
X-RAY DIFFRACTIONn_plane_restr0.010.02
X-RAY DIFFRACTIONn_chiral_restr0.090.1
X-RAY DIFFRACTIONn_singtor_nbd0.0750.1
X-RAY DIFFRACTIONn_multtor_nbd0.090.1
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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