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- PDB-1d29: CRYSTAL STRUCTURE ANALYSIS OF THE B-DNA DODECAMER CGTGAATTCACG -

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Basic information

Entry
Database: PDB / ID: 1d29
TitleCRYSTAL STRUCTURE ANALYSIS OF THE B-DNA DODECAMER CGTGAATTCACG
ComponentsDNA (5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLarsen, T.A. / Kopka, M.L. / Dickerson, R.E.
CitationJournal: Biochemistry / Year: 1991
Title: Crystal structure analysis of the B-DNA dodecamer CGTGAATTCACG.
Authors: Larsen, T.A. / Kopka, M.L. / Dickerson, R.E.
History
DepositionMay 23, 1991Deposition site: BNL / Processing site: BNL
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*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.940, 40.780, 66.130
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*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3')


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.23 mMDNA1drop
23.8 mMMagnesium acetate1drop
30.8 mMspermine1drop
413 %MPD1drop
527.5 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 273 K
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 1835 / Num. obs: 1475
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. measured all: 1835

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→10 Å /
RfactorNum. reflection
obs0.158 1475
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 36 522
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 1475 / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.1 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr

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