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- PDB-252d: CRYSTAL STRUCTURE OF THE B-DNA DECAMER D(CGCAATTGCG)2; SEQUENCE-D... -

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Basic information

Entry
Database: PDB / ID: 252d
TitleCRYSTAL STRUCTURE OF THE B-DNA DECAMER D(CGCAATTGCG)2; SEQUENCE-DEPENDENT CROSSED HELIX PACKING
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsWood, A.A. / Nunn, C.M. / Trent, J.O. / Neidle, S.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Sequence-dependent crossed helix packing in the crystal structure of a B-DNA decamer yields a detailed model for the Holliday junction.
Authors: Wood, A.A. / Nunn, C.M. / Trent, J.O. / Neidle, S.
#1: Journal: Biochemistry / Year: 1995
Title: Crystal Structure of C-T-C-T-C-G-A-G-A-G. Implications for the Structure of the Holliday Junction
Authors: Goodsell, D.S. / Grzeskowiak, K. / Dickerson, R.E.
History
DepositionMar 7, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 9, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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*AP*TP*TP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.630, 24.700, 38.290
Angle α, β, γ (deg.)90.00, 110.27, 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*AP*TP*TP*GP*CP*G)-3')


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 292.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5HOECHST 3325811
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mMDNA duplex1drop
2200 mM1dropMgCl2
340 %(v/v)MPD1drop
430 mMsodium cacodylate1drop
59.8 mMminor groove binding drug Hoechst 332581drop
640 %(v/v)MPD1reservoir
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Aug 3, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→8 Å / Num. all: 5015 / Num. obs: 2304 / % possible obs: 78 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.043
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 4 Å / % possible obs: 78 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.34 Å / % possible obs: 40.2 % / Rmerge(I) obs: 0.131

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rwork0.177 ---
obs0.177 2095 85 %-
Rfree---20.8
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 75 479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.81

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