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- PDB-290d: CRYSTAL STRUCTURES OF OLIGODEOXYRIBONUCLEOTIDES CONTAINING 6'-ALP... -

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Basic information

Entry
Database: PDB / ID: 290d
TitleCRYSTAL STRUCTURES OF OLIGODEOXYRIBONUCLEOTIDES CONTAINING 6'-ALPHA-METHYL AND 6'-ALPHA-HYDROXY CARBOCYCLIC THYMIDINES
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / CARBOCYCLUS / ANTISENSE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsPortmann, S. / Altmann, K.-H. / Reynes, N. / Egli, M.
CitationJournal: J.Am.Chem.Soc. / Year: 1997
Title: Crystal Structures of Oligodeoxyribonucleotides Containing 6'-alpha-Methyl and 6'-alpha-Hydroxy Carbocyclic Thymidines
Authors: Portmann, S. / Altmann, K.-H. / Reynes, N. / Egli, M.
History
DepositionOct 10, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 12, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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*(T32)P*(T32)P*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3752
Polymers7,3752
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.196, 40.798, 66.265
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*(T32)P*(T32)P*CP*GP*CP*G)-3')


Mass: 3687.500 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.9 / Details: pH 6.90, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MG ACETATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 mMDNA1drop
220 mMsodium cacodylate1drop
318.8 mM1dropMg(OAc)2
40.7 mMspermine tetrachloride1drop
540 %MPD1reservoir
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRmerge(I) obs: 0.035
Reflection
*PLUS
Highest resolution: 2.5 Å

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: BDL001

Resolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflection
Rfree0.292 -
Rwork0.17 -
obs0.17 2072
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 482 8 65 555
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_deg3.7
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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