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- PDB-287d: X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR ... -

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Basic information

Entry
Database: PDB / ID: 287d
TitleX-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsEisenstein, M. / Shatzky-Schwartz, M. / Shakked, Z.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature.
Authors: Shatzky-Schwartz, M. / Arbuckle, N.D. / Eisenstein, M. / Rabinovich, D. / Bareket-Samish, A. / Haran, T.E. / Luisi, B.F. / Shakked, Z.
History
DepositionSep 20, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0May 8, 1997Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.279, 39.355, 66.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlDNA1drop
215 mM1dropMgCl2
31.4 mMspermine 4HCl1drop
410 mMsodium cacodylate1drop
510 %(w/v)MPD1drop
630 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 100 K
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 2781 / % possible obs: 59.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.061
Reflection
*PLUS
Highest resolution: 2.2 Å
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 43 %

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.15 2292
Displacement parametersBiso mean: 8.9 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 137 623
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection all: 2781 / σ(F): 2 / Rfactor all: 0.193 / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 8.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.01
X-RAY DIFFRACTIONn_angle_d0.03

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