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- PDB-254d: ALTERNATING AND NON-ALTERNATING DG-DC HEXANUCLEOTIDES CRYSTALLIZE... -

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Basic information

Entry
Database: PDB / ID: 254d
TitleALTERNATING AND NON-ALTERNATING DG-DC HEXANUCLEOTIDES CRYSTALLIZE AS CANONICAL A-DNA
ComponentsDNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMooers, B.H. / Schroth, G.P. / Baxter, W.W. / Ho, P.S.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Alternating and non-alternating dG-dC hexanucleotides crystallize as canonical A-DNA.
Authors: Mooers, B.H. / Schroth, G.P. / Baxter, W.W. / Ho, P.S.
History
DepositionSep 29, 1995Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 15, 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(*GP*(5CM)P*GP*(5CM)P*GP*C)-3')
B: DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)3,6772
Polymers3,6772
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.670, 45.980, 39.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-33-

HOH

21A-43-

HOH

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Components

#1: DNA chain DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*C)-3')


Mass: 1838.259 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE11
5MGCL211
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMDNA1drop
215 mMsodium cacodylate1drop
30.5-5 mMspermine1drop
41-20 mM1dropMgCl2
55 %(v/v)MPD1drop
635 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→32 Å / Num. all: 2937 / Num. obs: 2937 / % possible obs: 68.3 % / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 32 Å / % possible obs: 68.3 % / Observed criterion σ(I): 2

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.186 --
Rwork0.197 --
obs0.197 1994 76.9 %
Displacement parametersBiso mean: 20.2 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 4 34 278
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_deg3.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d34.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.84
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: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg34.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.84

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