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- PDB-237d: CRYSTAL STRUCTURE OF A DNA DECAMER SHOWING A NOVEL PSEUDO FOUR-WA... -

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Basic information

Entry
Database: PDB / ID: 237d
TitleCRYSTAL STRUCTURE OF A DNA DECAMER SHOWING A NOVEL PSEUDO FOUR-WAY HELIX-HELIX JUNCTION
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / FLIPPED-OUT BASES / INTERMOLECULAR BASE TRIPLET
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSpink, N. / Nunn, C.M. / Vojtechovsky, J. / Berman, H.M. / Neidle, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction.
Authors: Spink, N. / Nunn, C.M. / Vojtechovsky, J. / Berman, H.M. / Neidle, S.
History
DepositionSep 28, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Mar 22, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,0451
Polymers3,0451
Non-polymers00
Water86548
1
A: DNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3')

A: 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Unit cell
Length a, b, c (Å)27.010, 39.260, 54.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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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.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 287.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5BERENIL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 287 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mMsodium cacodylate1drop
22.0 M1drop0.001mlMgCl2
349 %MPD1drop0.003ml
43 mMdecamer1drop0.004ml
515 mMminor-groove-binding drug berenil1drop0.002ml
650 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 10180 / Num. obs: 1521
Reflection
*PLUS
Observed criterion σ(I): 0 / Rmerge(I) obs: 0.102

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.212 --
obs0.212 957 94 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 0 48 250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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