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- PDB-9jl7: Crystal structure of Actinomycin D-Doxorubicin-d(AGCCGT)2 DNA ter... -

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Basic information

Entry
Database: PDB / ID: 9jl7
TitleCrystal structure of Actinomycin D-Doxorubicin-d(AGCCGT)2 DNA ternary complex
Components
  • Actinomycin D
  • DNA (5'-D(P*AP*CP*GP*GP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*CP*GP*T)-3')
KeywordsDNA/ANTIBIOTIC / Drug-DNA complex / Actinomycin D / Doxorubicin / DNA / DNA-ANTIBIOTIC complex
Function / homologyActinomycin D / DOXORUBICIN / : / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
Streptomyces parvulus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsLi, H.J. / Satange, R.B. / Hou, M.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2628-M-005-001-MY4 Taiwan
CitationJournal: J.Med.Chem. / Year: 2025
Title: Structural and Functional Insights into Targeting GCCG Sites in the EGFR Promoter by Two DNA Intercalators to Inhibit Breast Cancer Metastasis.
Authors: Chang, C.C. / Li, H.J. / Satange, R. / Lin, S.M. / Chen, T.L. / Lin, C.C. / Neidle, S. / Hou, M.H.
History
DepositionSep 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*AP*GP*CP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*GP*CP*T)-3')
G: Actinomycin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6548
Polymers4,9103
Non-polymers7445
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.002, 27.002, 205.993
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-102-

CL

21B-210-

HOH

31B-219-

HOH

41G-113-

HOH

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Components

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DNA chain , 2 types, 2 molecules AB

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*GP*CP*T)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide , 1 types, 1 molecules G

#3: Protein/peptide Actinomycin D


Type: Polypeptide / Class: Antibiotic / Mass: 1291.446 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (synth.) Streptomyces parvulus (bacteria) / References: NOR: NOR00228, Actinomycin D

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Non-polymers , 4 types, 95 molecules

#4: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO11 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has ligand of interestY
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.125mM duplex oligonucleotide, 0.125mM actinomycin D, 0.125mM doxorubicin, 30mM LiCl, 3mM MnCl2, 25mM MES (pH 6.5), 3% PEG 400

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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: Aug 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 7813 / % possible obs: 99.7 % / Redundancy: 34.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 38.8 % / Rmerge(I) obs: 0.449 / Num. unique obs: 729 / CC1/2: 0.994 / CC star: 0.998 / Rpim(I) all: 0.072 / Rrim(I) all: 0.455 / Χ2: 1.096 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→22.14 Å / SU ML: 0.11 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 772 10.01 %
Rwork0.2025 --
obs0.2038 7709 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→22.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90 246 43 90 469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012409
X-RAY DIFFRACTIONf_angle_d2.071617
X-RAY DIFFRACTIONf_dihedral_angle_d32.737142
X-RAY DIFFRACTIONf_chiral_restr0.98766
X-RAY DIFFRACTIONf_plane_restr0.01630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.620.26211210.21821091X-RAY DIFFRACTION100
1.62-1.740.24661240.19051107X-RAY DIFFRACTION100
1.74-1.910.23321250.19161126X-RAY DIFFRACTION100
1.92-2.190.24081260.21111131X-RAY DIFFRACTION100
2.19-2.760.20511320.22551189X-RAY DIFFRACTION100
2.76-22.140.19091440.19221293X-RAY DIFFRACTION99

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