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- PDB-7x6r: Crystal structure of actinomycin D-echinomycin-d(AGCACGT/ACGGGCT)... -

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Basic information

Entry
Database: PDB / ID: 7x6r
TitleCrystal structure of actinomycin D-echinomycin-d(AGCACGT/ACGGGCT) complex
Components
  • Actinomycin D
  • DNA (5'-D(P*AP*CP*GP*GP*GP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*CP*GP*T)-3')
  • DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
KeywordsDNA/ANTIBIOTIC / A:G mismatch / Single-strand DNA distortion / Actinomycin D / Echinomycin / mismatch binding drug / DNA / DNA-ANTIBIOTIC complex
Function / homologyActinomycin D / Echinomycin / : / 2-CARBOXYQUINOXALINE / DNA
Function and homology information
Biological speciesStreptomyces (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKao, S.H. / Satange, R.B. / 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: 2022
Title: Staggered intercalation of DNA duplexes with base-pair modulation by two distinct drug molecules induces asymmetric backbone twisting and structure polymorphism.
Authors: Satange, R. / Kao, S.H. / Chien, C.M. / Chou, S.H. / Lin, C.C. / Neidle, S. / Hou, M.H.
History
DepositionMar 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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*AP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*GP*GP*CP*T)-3')
C: Actinomycin D
D: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8869
Polymers6,3614
Non-polymers5255
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.225, 43.225, 65.839
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-101-

CO

21A-203-

HOH

31A-207-

HOH

41A-209-

HOH

51B-206-

HOH

61B-208-

HOH

71C-101-

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


Mass: 2122.424 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*GP*CP*T)-3')


Mass: 2138.423 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 (bacteria) / References: Actinomycin D
#4: Protein/peptide DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA


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 (bacteria) / References: Echinomycin

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Non-polymers , 3 types, 28 molecules

#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#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.: 23 / 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: 49.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.25 mM Oligonucleotide, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate (pH 6.5), 2.5 mM magnesium chloride, 2 mM spermine tetrahydrochloride, 6 mM cobalt chloride, 2% ...Details: 0.25 mM Oligonucleotide, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate (pH 6.5), 2.5 mM magnesium chloride, 2 mM spermine tetrahydrochloride, 6 mM cobalt chloride, 2% v/v PEG 200, 4% v/v MPD, Reservoir PEG 200 (30%)

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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: Jan 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. obs: 5402 / % possible obs: 99.4 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 43.112
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 10.111 / Num. unique obs: 71669 / Rsym value: 0.343

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DQ0

7dq0


Resolution: 1.89→27.723 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 538 10.05 %
Rwork0.2442 4817 -
obs0.2458 5355 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.05 Å2 / Biso mean: 49.3143 Å2 / Biso min: 24.23 Å2
Refinement stepCycle: final / Resolution: 1.89→27.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms155 289 15 23 482
Biso mean--36.88 50.29 -
Num. residues----34
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.89-2.07970.41151310.3222116999
2.0797-2.38050.30921320.2911117599
2.3805-2.99860.34521340.30791207100
2.9986-27.7230.21271410.2071126696
Refinement TLS params.Method: refined / Origin x: 59.4546 Å / Origin y: 51.6124 Å / Origin z: 82.6273 Å
111213212223313233
T0.3386 Å20.0183 Å20.0656 Å2-0.3165 Å20.02 Å2--0.2809 Å2
L4.9355 °2-2.5913 °2-2.0109 °2-6.5919 °24.9146 °2--6.3142 °2
S0.0381 Å °0.0173 Å °0.1909 Å °0.249 Å °-0.0314 Å °0.0977 Å °-0.0511 Å °-0.6867 Å °-0.0308 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 7
2X-RAY DIFFRACTION1allB1 - 7
3X-RAY DIFFRACTION1allC1 - 11
4X-RAY DIFFRACTION1allD1 - 10
5X-RAY DIFFRACTION1allE1 - 3
6X-RAY DIFFRACTION1allS1 - 34

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