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- PDB-7dq0: Crystal structure of actinomycin D-echinomycin-d(ACGTGCT/AGCTCGT)... -

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Basic information

Entry
Database: PDB / ID: 7dq0
TitleCrystal structure of actinomycin D-echinomycin-d(ACGTGCT/AGCTCGT) complex
Components
  • (DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)- ...) x 2
  • Actinomycin D
  • 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 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

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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*GP*CP*TP*CP*GP*T)-3')
C: Actinomycin D
D: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,90710
Polymers6,3274
Non-polymers5806
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-72 kcal/mol
Surface area2790 Å2
Unit cell
Length a, b, c (Å)30.188, 30.188, 137.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

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Components

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DNA (5'-D(P*AP*GP*CP*TP*CP*GP*T)- ... , 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*GP*CP*TP*CP*GP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide , 2 types, 2 molecules CD

#3: 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: NOR: NOR00228, Actinomycin D
#4: 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: NOR: NOR01126, Echinomycin

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Non-polymers , 4 types, 31 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 mM Sodium Cacodylate, 1 mM Magnesium chloride, 1 mM Spermine tetrahydrochloride, 1.5 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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 7257 / % possible obs: 98.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.012 / Rrim(I) all: 0.035 / Χ2: 0.831 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.078.30.234450.9960.0810.2440.76798.5
2.07-2.159.90.2224810.9980.0740.2350.73399.6
2.15-2.2511.30.1854580.9990.0580.1940.762100
2.25-2.3711.70.1574670.9980.0490.1650.77899.8
2.37-2.5211.50.1114870.9980.0350.1170.84599.8
2.52-2.7111.10.0814720.9980.0260.0850.8599.8
2.71-2.9910.60.04647410.0150.0490.77399.6
2.99-3.429.10.0274870.9990.0110.0290.90297
3.42-4.317.90.02150610.0080.0230.97797.9
4.31-306.30.0165530.9990.0070.0171.01596.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YTZ, 1MNV

5ytz

1mnv


Resolution: 2→25.22 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.66 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2494 716 9.87 %
Rwork0.2316 6541 -
obs0.2333 7257 88.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.57 Å2 / Biso mean: 28.3076 Å2 / Biso min: 11.96 Å2
Refinement stepCycle: final / Resolution: 2→25.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms155 286 16 25 482
Biso mean--26.68 26.61 -
Num. residues----34
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.150.273980.284488698459
2.15-2.370.28761340.26591251138585
2.37-2.710.30981640.266214891653100
2.71-3.410.25071610.24361460162199
3.41-25.220.20851590.19221455161498

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