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- PDB-1d31: THE THREE-DIMENSIONAL STRUCTURES OF BULGE-CONTAINING DNA FRAGMENTS -

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Basic information

Entry
Database: PDB / ID: 1d31
TitleTHE THREE-DIMENSIONAL STRUCTURES OF BULGE-CONTAINING DNA FRAGMENTS
ComponentsDNA (5'-D(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / BULGES / FLIPPED-OUT BASE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsJoshua-Tor, L. / Frolow, F. / Appella, E. / Hope, H. / Rabinovich, D. / Sussman, J.L.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Three-dimensional structures of bulge-containing DNA fragments.
Authors: Joshua-Tor, L. / Frolow, F. / Appella, E. / Hope, H. / Rabinovich, D. / Sussman, J.L.
#1: Journal: Nature / Year: 1988
Title: The Three-Dimensional Structure of a DNA Duplex Containing Looped-out Bases
Authors: Joshua-Tor, L. / Rabinovich, D. / Hope, H. / Frolow, F. / Appella, E. / Sussman, J.L.
#2: Journal: J.Mol.Biol. / Year: 1986
Title: Crystallization of a DNA Tridecamer d(CGCAGAATTCGCG)
Authors: Saper, M.A. / Eldar, H. / Mizuuchi, K. / Nickol, J. / Appella, E. / Sussman, J.L.
History
DepositionApr 25, 1991Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 1992Provider: 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(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,9532
Polymers7,9532
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.480, 42.840, 25.160
Angle α, β, γ (deg.)90.00, 99.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 3976.599 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4MGCL211
5NA CACODYLATE11
6WATER12
7MPD12
8NACLSodium chloride12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 6792 / Num. obs: 5530
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.048

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Processing

Software
NameClassification
NUCLSQrefinement
X-PLORrefinement
RefinementResolution: 2.6→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.186 1640
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 528 0 23 551
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / σ(F): 3 / Rfactor obs: 0.186 / Num. reflection obs: 1640
Solvent computation
*PLUS
Displacement parameters
*PLUS

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