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- PDB-233d: THE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC D... -

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Basic information

Entry
Database: PDB / ID: 233d
TitleTHE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC DNA DODECAMER DUPLEX CONTAINING FOUR 4'-THIO-2'-DEOXYTHYMIDINE NUCLEOTIDES
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*)-D(*(T49)P*(T49)P*)-D(*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsBoggon, T.J. / Hancox, E.L. / McAuley-Hecht, K.E. / Connolly, B.A. / Hunter, W.N. / Brown, T. / Walker, R.T. / Leonard, G.A.
CitationJournal: Nucleic Acids Res. / Year: 1996
Title: The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides.
Authors: Boggon, T.J. / Hancox, E.L. / McAuley-Hecht, K.E. / Connolly, B.A. / Hunter, W.N. / Brown, T. / Walker, R.T. / Leonard, G.A.
History
DepositionOct 16, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jun 21, 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 / 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*)-D(*(T49)P*(T49)P*)-D(*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*)-D(*(T49)P*(T49)P*)-D(*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3912
Polymers7,3912
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.993, 40.364, 65.993
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*)-D(*(T49)P*(T49)P*)-D(*CP*GP*CP*G)-3')


Mass: 3695.524 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMdodecanucleotide1drop
214 mMsodium cacodylate1drop
317 mMmagnesium chloride1drop
41 mMspermine tetrahydrochloride1drop
517 %(v/v)MPD1drop
650 %MPD1reservoir
71

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 2820
Reflection
*PLUS
Highest resolution: 2.4 Å / Rmerge(I) obs: 0.065

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.4→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.201 -
obs0.201 2605
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 67 553
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.53
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: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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