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- PDB-7x97: Crystal structure of actinomycin D-echinomycin-d(AGCCCGT/ACGGGCT)... -

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Basic information

Entry
Database: PDB / ID: 7x97
TitleCrystal structure of actinomycin D-echinomycin-d(AGCCCGT/ACGGGCT) complex
Components
  • Actinomycin D
  • DNA (5'-D(P*AP*CP*GP*GP*GP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*CP*CP*GP*T)-3')
  • DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
KeywordsDNA/ANTIBIOTIC / C:G Watson-Crick base pair / Single-strand DNA twisting / Actinomycin D / Echinomycin / DNA-antibiotic complex / DNA
Function / homologyActinomycin D / Echinomycin / : / 2-CARBOXYQUINOXALINE / DNA
Function and homology information
Biological speciesStreptomyces (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_atom_id_2 / _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*CP*CP*GP*T)-3')
B: DNA (5'-D(P*AP*CP*GP*GP*GP*CP*T)-3')
G: DSN-ALA-N2C-MVA-DSN-ALA-NCY-MVA
C: Actinomycin D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,12314
Polymers6,3374
Non-polymers78510
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-110 kcal/mol
Surface area2880 Å2
Unit cell
Length a, b, c (Å)43.452, 43.452, 139.365
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-101-

ZN

21A-104-

K

31A-105-

CL

41A-205-

HOH

51A-215-

HOH

61B-203-

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*CP*GP*T)-3')


Mass: 2098.399 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 GC

#3: 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
#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 (bacteria) / References: Actinomycin D

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Non-polymers , 5 types, 36 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-QUI / 2-CARBOXYQUINOXALINE


Mass: 174.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.25 mM Oligonucleotides, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate (pH 6.5), 0.5 mM Spermine tetrahydrochloride, 6 mM Zinc chloride, 3.5 mM Potassium chloride, ...Details: 0.25 mM Oligonucleotides, 0.25 mM Echinomycin, 0.125 mM Actinomycin D, 2.5 mM Sodium cacodylate (pH 6.5), 0.5 mM Spermine tetrahydrochloride, 6 mM Zinc chloride, 3.5 mM Potassium chloride, PEG200 3% (v/v), Reservoir PEG 200 (30% v/v)

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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: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 7161 / % possible obs: 97.8 % / Redundancy: 12.3 % / Biso Wilson estimate: 19.74 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.018 / Rrim(I) all: 0.06 / Χ2: 0.888 / Net I/σ(I): 7.7 / Num. measured all: 76141
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.399 / Num. unique obs: 702 / CC1/2: 0.999 / Rpim(I) all: 0.01 / Rrim(I) all: 0.034 / Χ2: 0.859 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DQ0

7dq0


Resolution: 1.95→25.57 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 701 9.79 %
Rwork0.229 6460 -
obs0.234 7161 66.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.56 Å2 / Biso mean: 25.47 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 1.95→25.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms143 287 32 26 488
Biso mean--18.52 22.18 -
Num. residues----33
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 (%)
1.9504-2.10090.3545610.269956963029
2.1009-2.31220.3478780.276981289041
2.3122-2.64650.31581390.28471250138965
2.6465-3.33310.31092140.25631929214399
3.3331-25.50.23662090.18331900210998
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)
13.28620.5018-1.273.36070.74710.75970.0247-0.0949-0.01410.1580.0074-0.00890.1758-0.11270.00320.19090.1044-0.01530.1223-0.01940.118.2646-5.6228-16.6574
21.96621.10262.12151.9340.96772.32490.05960.14180.14290.07130.3248-0.188-0.43540.5174-0.38720.4888-0.08990.0210.1574-0.0140.142225.078-0.1223-17.1787
33.423-0.60240.8531.57970.90390.96630.15380.23540.2572-0.5342-0.1635-0.0903-0.2478-0.0693-0.0020.39430.10680.00670.1218-0.00410.14920.74440.7312-22.6358
42.8505-0.92870.34291.91081.00710.8242-0.1498-0.13370.20470.0473-0.11720.2964-0.2853-0.22440.2440.30590.13460.00840.192-0.01250.162217.4853-0.3845-8.413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 7 )A0
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 1 THROUGH 7 )B0
3X-RAY DIFFRACTION3CHAIN 'G' AND (RESID 2 THROUGH 6 )G0
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 1 THROUGH 9 )C0

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