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- PDB-191d: CRYSTAL STRUCTURE OF INTERCALATED FOUR-STRANDED D(C3T) -

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Basic information

Entry
Database: PDB / ID: 191d
TitleCRYSTAL STRUCTURE OF INTERCALATED FOUR-STRANDED D(C3T)
ComponentsDNA (5'-D(*CP*CP*CP*T)-3')
KeywordsDNA / U-DNA / QUADRUPLE HELIX / PARALLEL-STRANDED TETRAPLEX / BASE INTERCALATED / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsKang, C. / Berger, I. / Lockshin, C. / Ratliff, R. / Moyzis, R. / Rich, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution.
Authors: Kang, C.H. / Berger, I. / Lockshin, C. / Ratliff, R. / Moyzis, R. / Rich, A.
History
DepositionSep 29, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2012Group: Other
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,5767
Polymers4,5074
Non-polymers693
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.281, 44.341, 50.472
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-20-

HOH

21D-81-

HOH

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Components

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


Mass: 1126.781 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.76 Å3/Da / Density % sol: 29.93 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5SRCL211
6SR CACODYLATE11
7WATER12
8MPD12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.3 mMsodium salt1drop
220 mM1dropMgCl2
30.12 mMspermine1drop
480 mM1dropSrCl2
540 mMstrontium cacodylate1drop
610 %MPD1drop
730 %MPD1reservoir
81

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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
ReflectionHighest resolution: 1.4 Å

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.4→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.225 --
Rwork0.177 --
obs0.177 5013 96 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 296 3 63 362
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.029
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_deg4
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: 1.4 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.177 / Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 4

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