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- PDB-218d: THE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING... -

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Basic information

Entry
Database: PDB / ID: 218d
TitleTHE STRUCTURE OF A NEW CRYSTAL FORM OF A DNA DODECAMER CONTAINING T.(O6ME)G BASE PAIRS
ComponentsDNA (5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsVojtechovsky, J. / Eaton, M.D. / Gaffney, B. / Jones, R. / Berman, H.M.
CitationJournal: Biochemistry / Year: 1995
Title: Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs.
Authors: Vojtechovsky, J. / Eaton, M.D. / Gaffney, B. / Jones, R. / Berman, H.M.
History
DepositionJul 18, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 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*TP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3852
Polymers7,3852
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.120, 38.810, 64.480
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*TP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3')


Mass: 3692.430 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.87 Å3/Da / Density % sol: 34.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 296.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 23 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.0 mMDNA1drop
220 mMsodium cacodylate1drop
320 mM1dropMgCl2
415 %MPD1drop
530 %MPD1reservoir
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.97 Å / Num. all: 4218 / Num. obs: 2387 / % possible obs: 99.5 % / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.97 Å / % possible obs: 99.5 % / Observed criterion σ(F): 2

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.25→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.167 -
obs0.167 2040
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 2 74 564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.81
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: 2.25 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_dihedral_angle_deg19.6
X-RAY DIFFRACTIONx_improper_angle_deg1.82

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