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- PDB-9v89: Crystal structure of d(CGTTAACG)2 with a five-carbon linker conta... -

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Basic information

Entry
Database: PDB / ID: 9v89
TitleCrystal structure of d(CGTTAACG)2 with a five-carbon linker containing quinoxaline-acridine asymmetric intercalator compound
ComponentsDNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
KeywordsDNA / Ligand-DNA complex / Asymmetric intercalator / Bis-intercalation / Quinoxaline / Acridine
Function / homology: / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsWang, S.C. / Hou, M.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2628-M-005-001-MY4 Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2311-B-005-007-MY3 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Structural basis for asymmetric bis-intercalator targeting of DNA triplex junctions enabling dual inhibition of topoisomerase I and oncogene transcription.
Authors: Wang, S.C. / Hsieh, C.C. / Yuan, T.C. / Lin, S.M. / Chen, C.W. / Chang, C.C. / Huang, S.C. / Wang, E.C. / Huang, Y.J. / Chiang, M.H. / Horng, Y.C. / Hou, M.H.
History
DepositionMay 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
B: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5256
Polymers4,8532
Non-polymers6724
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-20 kcal/mol
Surface area4140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.835, 34.948, 47.901
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(P*CP*GP*TP*TP*AP*AP*CP*G)-3')


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-W1H / N-[5-(acridin-9-ylamino)pentyl]quinoxaline-2-carboxamide


Mass: 435.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.6mM oligonucleotides, 0.6mM QA5, 50mM 2-(N-morpholino)ethanesulfonic acid hydrate (pH 6.5), 200mM potassium chloride, 5mM hexammine cobalt(III) chloride, 15% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.27→30 Å / Num. obs: 10857 / % possible obs: 97.5 % / Redundancy: 5.9 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.028 / Rrim(I) all: 0.066 / Χ2: 1.054 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.27-1.326.40.20310520.9730.9930.0860.2211.03896.8
1.32-1.376.30.17610450.9730.9930.0760.1931.08996.7
1.37-1.436.40.15210340.9790.9950.0650.1661.09395.8
1.43-1.516.30.12710600.9870.9970.0550.1391.00597.1
1.51-1.66.10.10511050.990.9980.0470.1151.07898.7
1.6-1.725.80.08310740.9920.9980.0390.0921.07198.3
1.72-1.95.70.07310700.9940.9980.0340.0811.03497.3
1.9-2.175.50.06310990.9950.9990.0290.071.0197.7
2.17-2.745.70.05511230.9970.9990.0250.0611.0899.1
2.74-305.10.0511950.9960.9990.0250.0561.03597.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIX(1.20.1_4487)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→23.95 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 1081 10.01 %
Rwork0.2123 --
obs0.2141 10803 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→23.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 328 43 80 451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011410
X-RAY DIFFRACTIONf_angle_d1.43620
X-RAY DIFFRACTIONf_dihedral_angle_d34.419163
X-RAY DIFFRACTIONf_chiral_restr0.05965
X-RAY DIFFRACTIONf_plane_restr0.01419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.330.28951310.25191180X-RAY DIFFRACTION96
1.33-1.40.24531300.23921165X-RAY DIFFRACTION96
1.4-1.490.25111320.22591193X-RAY DIFFRACTION97
1.49-1.60.25111350.21441214X-RAY DIFFRACTION98
1.6-1.760.19981340.18931206X-RAY DIFFRACTION98
1.76-2.020.23341350.2021212X-RAY DIFFRACTION98
2.02-2.540.25991370.23391239X-RAY DIFFRACTION98
2.54-23.950.20911470.20341313X-RAY DIFFRACTION98

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