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- PDB-1d59: CRYSTAL STRUCTURE OF 4-STRANDED OXYTRICHA TELOMERIC DNA -

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Basic information

Entry
Database: PDB / ID: 1d59
TitleCRYSTAL STRUCTURE OF 4-STRANDED OXYTRICHA TELOMERIC DNA
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
KeywordsDNA / U-DNA / QUADRUPLE HELIX / TETRAPLEX / LOOP
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKang, C. / Zhang, X. / Ratliff, R. / Moyzis, R. / Rich, A.
CitationJournal: Nature / Year: 1992
Title: Crystal structure of four-stranded Oxytricha telomeric DNA.
Authors: Kang, C. / Zhang, X. / Ratliff, R. / Moyzis, R. / Rich, A.
History
DepositionFeb 25, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,2224
Polymers15,2224
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6112
Polymers7,6112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')
D: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,6112
Polymers7,6112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.730, 49.570, 97.270
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(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')


Mass: 3805.460 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5K CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMoligonucleotide1drop
210 mM1dropMgCl2
36 mMspermine1drop
440 mM1dropKCl
520 mMpotassium cacodylate1drop
65 %MPD1drop
740 %1reservoir

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Data collection

DetectorType: SDMS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. all: 4963 / Num. obs: 2471 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2.3 Å / Observed criterion σ(F): 2 / Num. measured all: 6322

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.3→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.195 -
obs0.195 2471
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1132 0 0 1132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.99
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: 2.3 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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