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- PDB-190d: Crystal structure of a four-stranded intercalated DNA: d(C4) -

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Basic information

Entry
Database: PDB / ID: 190d
TitleCrystal structure of a four-stranded intercalated DNA: d(C4)
ComponentsDNA (5'-D(*CP*CP*CP*C)-3')
KeywordsDNA / U-DNA / QUADRUPLE HELIX / PARALLEL-STRANDED TETRAPLEX / BASE INTERCALATED / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsChen, L. / Cai, L. / Zhang, X. / Rich, A.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of a four-stranded intercalated DNA: d(C4).
Authors: Chen, L. / Cai, L. / Zhang, X. / Rich, A.
History
DepositionSep 2, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 7, 1995Provider: 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

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*CP*C)-3')
B: DNA (5'-D(*CP*CP*CP*C)-3')
C: DNA (5'-D(*CP*CP*CP*C)-3')
D: DNA (5'-D(*CP*CP*CP*C)-3')
E: DNA (5'-D(*CP*CP*CP*C)-3')
F: DNA (5'-D(*CP*CP*CP*C)-3')
G: DNA (5'-D(*CP*CP*CP*C)-3')
H: DNA (5'-D(*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)8,8948
Polymers8,8948
Non-polymers00
Water82946
1
A: DNA (5'-D(*CP*CP*CP*C)-3')
B: DNA (5'-D(*CP*CP*CP*C)-3')
C: DNA (5'-D(*CP*CP*CP*C)-3')
D: DNA (5'-D(*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,4474
Polymers4,4474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*CP*CP*C)-3')
F: DNA (5'-D(*CP*CP*CP*C)-3')
G: DNA (5'-D(*CP*CP*CP*C)-3')
H: DNA (5'-D(*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,4474
Polymers4,4474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint7.1 kcal/mol
Surface area1490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.300, 82.300, 82.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: DNA chain
DNA (5'-D(*CP*CP*CP*C)-3')


Mass: 1111.770 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4WATER12
5MPD12
Crystal grow
*PLUS
pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.7 mMd(C4)1drop
2100 mMsodium cacodylate1drop
320 %MPD1reservoir
41
51

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.8→8 Å / σ(F): 2
Details: THIS IS THE FIRST X-RAY STRUCTURE OF THE INTERCALATED CYTOSINE QUADRUPLEX. THE PAPER CITED IN JRNL DESCRIBED THE D(C4) STRUCTURE REFINED AT 2.3 ANGSTROMS RESOLUTION. THE AUTHORS HAVE ...Details: THIS IS THE FIRST X-RAY STRUCTURE OF THE INTERCALATED CYTOSINE QUADRUPLEX. THE PAPER CITED IN JRNL DESCRIBED THE D(C4) STRUCTURE REFINED AT 2.3 ANGSTROMS RESOLUTION. THE AUTHORS HAVE EXTENDED THE STRUCTURE DETERMINATION TO 1.8 ANGSTROMS RESOLUTION AND THE COORDINATES DEPOSITED ARE THE FINAL 1.8 ANGSTROMS STRUCTURE WHICH IS BASICALLY THE SAME AS THAT AT 2.3 ANGSTROMS RESOLUTION. THERE ARE 8 D(C4) STRANDS PER ASYMMETRIC UNIT WHICH FORM TWO TETRAMERS. THE FIRST TETRAMER IS NUMBERED FROM 1 TO 16, AND THE OTHER TETRAMER FROM 17 TO 32. THERE ARE 46 WATER MOLECULES FOUND AT 1.8 A RESOLUTION. ALL HYDROGEN ATOMS ARE INCLUDED FOR EASY REFERENCE ALTHOUGH THEY ARE NOT REFINED WITH X-RAY DATA. THE STRUCTURE WAS SOLVED BY HEAVY ATOM PHASING. K2PTCL6 WAS SOAKED INTO THE CRYSTAL AND ONLY ONE PT SITE WAS FOUND WHICH WAS AT THE THREE-FOLD AXIS. SINGLE ISOMORPHOUS REPLACEMENT (SIR) PHASES AND SINGLE-WAVELENGTH ANOMALOUS SCATTERING (SAS) PHASES WERE IMPROVED BY SOLVENT FLATTENING. THE RESULTANT ELECTRON DENSITY MAP CLEARLY REVEALED THE INTERCALATED STRUCTURE FOR THE FIRST TIME.
RfactorNum. reflection% reflection
Rwork0.218 --
obs0.218 8177 95.1 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 952 0 138 1090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection obs: 4051 / Rfactor obs: 0.188 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg3.6

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