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- PDB-1vtg: THE MOLECULAR STRUCTURE OF A DNA-TRIOSTIN A COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1vtg
TitleTHE MOLECULAR STRUCTURE OF A DNA-TRIOSTIN A COMPLEX
Components
  • DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
  • triostin A
KeywordsDNA/ANTIBIOTIC / BISINTERCALATOR / DEPSIPEPTIDE / QUINOXALINE / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX
Function / homologyTRIOSTIN A / 2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciessynthetic construct (others)
Streptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.67 Å
AuthorsWang, A.H.-J. / Ughetto, G. / Quigley, G.J. / Hakoshima, T. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A.
Citation
Journal: Science / Year: 1984
Title: The molecular structure of a DNA-triostin A complex.
Authors: Wang, A.H. / Ughetto, G. / Quigley, G.J. / Hakoshima, T. / van der Marel, G.A. / van Boom, J.H. / Rich, A.
#1: Journal: Nucleic Acids Res. / Year: 1985
Title: A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment.
Authors: Ughetto, G. / Wang, A.H. / Quigley, G.J. / van der Marel, G.A. / van Boom, J.H. / Rich, A.
#2: Journal: J. Biomol. Struct. Dyn. / Year: 1986
Title: Interactions of quinoxaline antibiotic and DNA: the molecular structure of a triostin A-d(GCGTACGC) complex.
Authors: Wang, A.H. / Ughetto, G. / Quigley, G.J. / Rich, A.
History
DepositionAug 18, 1988Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Derived calculations / Structure summary
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 10, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / pdbx_entity_src_syn / pdbx_validate_polymer_linkage
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
B: triostin A
B: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,9534
Polymers2,6042
Non-polymers3482
Water00
1
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
B: triostin A
hetero molecules

A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
B: triostin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9058
Polymers5,2084
Non-polymers6974
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)31.350, 62.380, 61.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: DNA chain DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide triostin A


Type: Cyclic depsipeptide / Class: Anticancer / Mass: 794.982 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Source: (synth.) Streptomyces sp. (bacteria) / References: NOR: NOR01129, TRIOSTIN A
#3: Chemical ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Anticancer / Mass: 174.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O2
Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: TRIOSTIN A
Compound detailsTRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ...TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, TRIOSTIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) QUI GROUP: 1 NAME: TRIOSTIN CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 8 COMPONENT_2: QUINALDIC ACID CHROMOPHORE RESIDUES 0 AND 9 DESCRIPTION: TRIOSTIN IS A IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.28 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38NA CACODYLATE1917
411MGCL2112110
514WATER115213
617MPD118216

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Data collection

DiffractionMean temperature: 257 K
DetectorType: NICOLET P3 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 2995 / Observed criterion σ(I): 1

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementRfactor obs: 0.189 / Highest resolution: 1.67 Å
Details: COORDINATES ARE REPORTED IN THE JRNL REFERENCE PAPER AS A COMPARISON.
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Highest resolution: 1.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52 120 24 0 196

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