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- PDB-9v87: Crystal structure of d(CGTTAACG)2 -

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Basic information

Entry
Database: PDB / ID: 9v87
TitleCrystal structure of d(CGTTAACG)2
ComponentsDNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
KeywordsDNA / DNA perfectly matched / Watson and Crick base pairing
Function / homology: / SPERMINE (FULLY PROTONATED FORM) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsYuan, Y.C. / Wang, 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')
C: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*TP*TP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,56714
Polymers9,7064
Non-polymers86110
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.447, 45.447, 71.352
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11B-103-

CL

21C-202-

CO

31A-204-

HOH

41A-207-

HOH

51A-211-

HOH

61A-215-

HOH

71B-211-

HOH

81C-308-

HOH

91C-318-

HOH

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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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SPK / SPERMINE (FULLY PROTONATED FORM)


Mass: 206.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H30N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.6mM Oligonucleotide, 50mM HEPES pH 7.5, 2mM Spermine tetrahydrochloride, 8.5mM Cobalt(II) chloride, 5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→30 Å / Num. obs: 11151 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.61-1.675.30.34211080.9930.9980.1650.381.068100
1.67-1.735.50.44511010.9230.980.2070.4921.051100
1.73-1.815.50.30611030.9530.9880.1430.3381.08599.9
1.81-1.915.50.2411030.9750.9940.1110.2651.095100
1.91-2.035.50.18211110.9760.9940.0850.2011.085100
2.03-2.185.50.12511040.9870.9970.0580.1391.09399.9
2.18-2.45.50.08711220.9950.9990.040.0961.049100
2.4-2.755.50.04911090.9970.9990.0230.0541.044100
2.75-3.475.50.0271128110.0130.031.04399.1
2.75-3.475.30.02211620.99910.0110.0251.06498.3

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→18.97 Å / Cross valid method: NONE / σ(F): 1.35 / Phase error: 35.49 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2539 1108 9.96 %
Rwork0.213 --
obs0.2565 11122 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→18.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 599 36 66 701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008695
X-RAY DIFFRACTIONf_angle_d0.8381048
X-RAY DIFFRACTIONf_dihedral_angle_d32.529332
X-RAY DIFFRACTIONf_chiral_restr0.045116
X-RAY DIFFRACTIONf_plane_restr0.00529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.680.42251390.42711255X-RAY DIFFRACTION90
1.68-1.770.39521340.38641221X-RAY DIFFRACTION90
1.77-1.880.34171400.391248X-RAY DIFFRACTION90
1.88-2.030.33511340.34831237X-RAY DIFFRACTION90
2.03-2.230.3521390.29831250X-RAY DIFFRACTION90
2.23-2.550.30961400.29691255X-RAY DIFFRACTION90
2.55-3.210.26421400.24361258X-RAY DIFFRACTION90
3.22-18.970.24121410.16981291X-RAY DIFFRACTION89

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