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- PDB-7bna: ANISOTROPIC THERMAL-PARAMETER REFINEMENT OF THE DNA DODECAMER CGC... -

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Basic information

Entry
Database: PDB / ID: 7bna
TitleANISOTROPIC THERMAL-PARAMETER REFINEMENT OF THE DNA DODECAMER CGCGAATTCGCG BY THE SEGMENTED RIGID-BODY METHOD
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHolbrook, S.R. / Dickerson, R.E. / Kim, S.-H.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1985
Title: Anisotropic Thermal-Parameter Refinement of the DNA Dodecamer CGCGAATTCGCG by the Segmented Rigid-Body Method
Authors: Holbrook, S.R. / Dickerson, R.E. / Kim, S.-H.
#1: Journal: J.Mol.Biol. / Year: 1984
Title: Local Mobility of Nucleic Acids as Determined from Crystallographic Data. I. RNA and B Form DNA
Authors: Holbrook, S.R. / Kim, S.-H.
#2: Journal: Nature / Year: 1980
Title: Crystal Structure Analysis of a Complete Turn of B-DNA
Authors: Wing, R. / Drew, H.R. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionJan 7, 1985Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 17, 1985Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 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*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.870, 40.390, 66.200
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*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.: 78 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, temperature 290.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MG ACETATE11
3SPERMINE_HCL11
4WATER12
5MPD12
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51

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Data collection

DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 5691
Reflection
*PLUS
Highest resolution: 1.9 Å / Rmerge(I) obs: 0.264

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementResolution: 1.9→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.149 2728
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRanisotropic
ALL WATERSX-RAY DIFFRACTIONTRanisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 78 564
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection all: 5599 / σ(F): 2 / Rfactor all: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS

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