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- PDB-3bna: REVERSIBLE BENDING AND HELIX GEOMETRY IN A B-DNA DODECAMER: CGCGA... -

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Basic information

Entry
Database: PDB / ID: 3bna
TitleREVERSIBLE BENDING AND HELIX GEOMETRY IN A B-DNA DODECAMER: CGCGAATTBRCGCG
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsKopka, M.L. / Fratini, A.V. / Dickerson, R.E.
Citation
Journal: J.Biol.Chem. / Year: 1982
Title: Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.
Authors: Fratini, A.V. / Kopka, M.L. / Drew, H.R. / Dickerson, R.E.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Ordered Water Structure around a B-DNA Dodecamer. A Quantitative Study
Authors: Kopka, M.L. / Fratini, A.V. / Drew, H.R. / Dickerson, R.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Structure of a B-DNA Dodecamer at 16 Kelvin
Authors: Drew, H.R. / Samson, S. / Dickerson, R.E.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Kinematic Model for B-DNA
Authors: Dickerson, R.E. / Drew, H.R.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1981
Title: Structure of a B-DNA Dodecamer. Conformation and Dynamics
Authors: Drew, H.R. / Wing, R.M. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
#5: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of a B-DNA Dodecamer. II. Influence of Base Sequence on Helix Structure
Authors: Dickerson, R.E. / Drew, H.R.
#6: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of a B-DNA Dodecamer. III. Geometry of Hydration
Authors: Drew, H.R. / Dickerson, R.E.
#7: Journal: Nature / Year: 1980
Title: Crystal Structure Analysis of a Complete Turn of B-DNA
Authors: Wing, R. / Drew, H. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionFeb 16, 1982Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 15, 1982Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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*AP*TP*TP*(CBR)P*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,4852
Polymers7,4852
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.710, 40.560, 65.620
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*AP*TP*TP*(CBR)P*GP*CP*G)-3')


Mass: 3742.288 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 280 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 280.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG2+11
4SPERMINE11
Crystal grow
*PLUS
Temperature: 7 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
120-35 %(v/v)MPD1
2128Mg2+
31.3 spermine molecules1
412-base pair double helix1

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Data collection

DiffractionMean temperature: 293 K
DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→8 Å / Num. obs: 1515
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / Rmerge(I) obs: 0.39

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Processing

SoftwareName: JACK-LEVITT / Classification: refinement
RefinementResolution: 3→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.13 1515
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 2 44 532
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS

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