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- PDB-241d: EXTENSION OF THE FOUR-STRANDED INTERCALATED CYTOSINE MOTIF BY ADE... -

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Basic information

Entry
Database: PDB / ID: 241d
TitleEXTENSION OF THE FOUR-STRANDED INTERCALATED CYTOSINE MOTIF BY ADENINE.ADENINE BASE PAIRING IN THE CRYSTAL STRUCTURE OF D(CCCAAT)
ComponentsDNA (5'-D(*CP*CP*CP*AP*AP*T)-3')
KeywordsDNA / U-DNA / QUADRUPLE HELIX / ARALLEL-STRANDED TETRAPLEX / BASE INTERCALATED / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsBerger, I. / Kang, C. / Fredian, A. / Ratliff, R. / Moyzis, R. / Rich, A.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: Extension of the four-stranded intercalated cytosine motif by adenine.adenine base pairing in the crystal structure of d(CCCAAT).
Authors: Berger, I. / Kang, C. / Fredian, A. / Ratliff, R. / Moyzis, R. / Rich, A.
History
DepositionDec 7, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 3, 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 / 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

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*CP*AP*AP*T)-3')
B: DNA (5'-D(*CP*CP*CP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,5062
Polymers3,5062
Non-polymers00
Water1,02757
1
A: DNA (5'-D(*CP*CP*CP*AP*AP*T)-3')
B: DNA (5'-D(*CP*CP*CP*AP*AP*T)-3')

A: DNA (5'-D(*CP*CP*CP*AP*AP*T)-3')
B: DNA (5'-D(*CP*CP*CP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,0134
Polymers7,0134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)32.180, 32.180, 52.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-23-

HOH

21B-63-

HOH

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Components

#1: DNA chain DNA (5'-D(*CP*CP*CP*AP*AP*T)-3')


Mass: 1753.194 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE11
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %MPD1drop
20.1 mMspermine1drop
380 mMNa-cacodylate1drop
42 mMDNA1drop
535 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 277 K
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.85→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 2285
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 232 0 57 289
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.028
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
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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