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- PDB-7dq8: Crystal structure of actinomycin D-echinomycin-d(ACGCGCT/AGCTCGT)... -

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Basic information

Entry
Database: PDB / ID: 7dq8
TitleCrystal structure of actinomycin D-echinomycin-d(ACGCGCT/AGCTCGT) complex
Components
  • Actinomycin D
  • DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)-3')
  • Echinomycin
KeywordsANTIBIOTIC/DNA / Drug-DNA complex / DNA mismatch / DNA unwinding / DNA deformation / DNA / ANTIBIOTIC-DNA complex
Function / homologyActinomycin D / Echinomycin / 2-CARBOXYQUINOXALINE / DNA
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSatange, R.B. / Hou, M.H.
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Synergistic binding of actinomycin D and echinomycin to DNA mismatch sites and their combined anti-tumour effects.
Authors: Satange, R. / Chang, C.C. / Li, L.Y. / Lin, S.H. / Neidle, S. / Hou, M.H.
History
DepositionDec 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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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*TP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')
D: Echinomycin
C: Actinomycin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,75810
Polymers6,3124
Non-polymers4466
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-18 kcal/mol
Surface area2810 Å2
Unit cell
Length a, b, c (Å)29.738, 29.738, 137.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-101-

MG

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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*TP*CP*GP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*CP*GP*CP*T)-3')


Mass: 2098.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide , 2 types, 2 molecules DC

#3: Protein/peptide Echinomycin


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 809.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Source: (natural) Streptomyces sp. (bacteria) / References: Echinomycin
#4: Protein/peptide Actinomycin D


Type: Polypeptide / Class: Antibiotic / Mass: 1291.446 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) Streptomyces sp. (bacteria) / References: Actinomycin D

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Non-polymers , 3 types, 18 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O2
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: Echinomycin
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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). THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI.
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 mM ssDNA, 0.2 mM echinomycin, 0.1 mM actinomycin D, 2.5 mM Sodium Cacodylate (pH 7.0), 1 mM magnesium chloride, 2.5 mM spermine tetrahydrochloride, 1 mM zinc chloride, 1% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 2811 / % possible obs: 99 % / Redundancy: 11.6 % / Biso Wilson estimate: 48.27 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 21.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.726 / Num. unique obs: 32688 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DQ0

7dq0


Resolution: 2.4→24.97 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 276 10.07 %
Rwork0.267 --
obs0.268 2741 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms143 285 28 12 468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.027489
X-RAY DIFFRACTIONf_angle_d2.105713
X-RAY DIFFRACTIONf_dihedral_angle_d40.714170
X-RAY DIFFRACTIONf_chiral_restr0.10974
X-RAY DIFFRACTIONf_plane_restr0.01440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4035-2.490.34781350.33611213X-RAY DIFFRACTION100
2.49-24.970.25991410.2451252X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.05590.7096-2.55233.2918-2.37865.18860.4564-0.6152-0.21960.40670.2896-0.2583-2.5132.3074-0.51080.2602-0.09860.04731.0323-0.10890.395412.94986.67385.3267
20.5613-0.36530.00322.7964-2.9268.52190.7040.4488-0.7976-0.03050.07380.69890.71981.711-0.68950.79430.041-0.03710.497-0.00620.410.9494-1.57723.9786
34.78372.2411-0.64083.1323-1.89286.91651.3235-0.60711.2141.2802-1.5554-1.13090.40232.1890.17760.2631-0.03490.02170.53410.16350.520915.7131.983814.0601
44.02473.44180.47883.2629-0.46612.68920.17460.2955-0.5088-0.51670.425-1.66830.30650.96520.00920.25150.29290.05280.6268-0.04120.529314.5250.349-4.904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 7 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 9 )
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 6 )

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