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- PDB-126d: CRYSTAL STRUCTURE OF CATGGCCATG AND ITS IMPLICATIONS FOR A-TRACT ... -

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Basic information

Entry
Database: PDB / ID: 126d
TitleCRYSTAL STRUCTURE OF CATGGCCATG AND ITS IMPLICATIONS FOR A-TRACT BENDING MODELS
ComponentsDNA (5'-D(*CP*AP*TP*GP*GP*CP*CP*AP*TP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsGoodsell, D.S. / Kopka, M.L. / Cascio, D. / Dickerson, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal structure of CATGGCCATG and its implications for A-tract bending models.
Authors: Goodsell, D.S. / Kopka, M.L. / Cascio, D. / Dickerson, R.E.
History
DepositionJun 14, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1993Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.600, 42.490, 34.690
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*AP*TP*GP*GP*CP*CP*AP*TP*G)-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.: 49 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 278.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3CACL211
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: vapor diffusionstanding drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.54 mMdecamer1dropdouble helix
2145 mM1dropCaCl2
34.5 mMspermine tetrahydrochloride1drop
415 %(v/v)MPD1drop
545 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 278 K
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 3217 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2 Å / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.053

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.196 3217
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 49 453
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 3217 / σ(F): 2 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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