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- PDB-281d: CRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GGCATGCC) -

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Basic information

Entry
Database: PDB / ID: 281d
TitleCRYSTAL STRUCTURE OF THE A-DNA OCTAMER D(GGCATGCC)
ComponentsDNA (5'-D(*GP*GP*CP*AP*TP*GP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.38 Å
AuthorsNunn, C.M. / Neidle, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structure of the A-DNA octamer d(GGCATGCC).
Authors: Nunn, C.M. / Neidle, S.
History
DepositionAug 23, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 16, 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 / 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*CP*AP*TP*GP*CP*C)-3')
B: DNA (5'-D(*GP*GP*CP*AP*TP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,8552
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)46.291, 46.291, 42.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 2427.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 287.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4NH4+11
5[CO(NH3)6]CL311
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 287 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mMDNA1drop0.005ml
230 mMsodium cacodylate1drop0.005ml
335 %(v/v)1drop0.002mlNH3
410 mMhexamminecobalt(III) trichloride1drop0.002 ml
540 %(v/v)MPD1drop
640 %(v/v)MPD1reservoir
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jan 11, 1996
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.38 Å / Num. all: 5252 / Num. obs: 2167 / % possible obs: 97 % / Rmerge(I) obs: 0.039
Reflection
*PLUS
Highest resolution: 2.38 Å / Num. all: 2167 / Num. obs: 2104 / % possible obs: 97 % / Num. measured all: 5252

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
XDSdata reduction
RefinementResolution: 2.38→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.171 -
obs0.171 2045
Displacement parametersBiso mean: 26 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.38→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 66 388
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.48
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.38 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26 Å2

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