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- PDB-193d: SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 193d
TitleSOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX
Components
  • DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*T)-3')
  • QUINOMYCIN
KeywordsDNA/ANTIBIOTIC / BISINTERCALATOR / DEPSIPEPTIDE / QUINOXALINE / THIOACETAL / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX
Function / homologyuk63052 / 3-HYDROXYQUINALDIC ACID / DNA
Function and homology information
Biological speciesSTREPTOMYCES (bacteria)
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsChen, H. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Solution Structure of a Quinomycin Bisintercalator-DNA Complex.
Authors: Chen, H. / Patel, D.J.
History
DepositionSep 30, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 2.0Nov 1, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_polymer_linkage
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_status.process_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*T)-3')
B: DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*T)-3')
C: QUINOMYCIN
C: 3-HYDROXYQUINALDIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0795
Polymers5,7003
Non-polymers3782
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: ALA D 2 - CYS D 3 MODEL 1 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 2 - CYS C 3 MODEL 2 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ALA D 2 - CYS D 3 MODEL 3 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ALA D 2 - CYS D 3 MODEL 4 OMEGA = 359.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: SER C 1 IS A D-SERINE. / 8: SER D 1 IS A D-SERINE.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4all calculated structures submitted
Representative

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Components

#1: DNA chain DNA (5'-D(*AP*CP*AP*CP*GP*TP*GP*T)-3')


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED
#2: Protein/peptide QUINOMYCIN / QUINOMYCIN A / UK-63052


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 847.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Source: (synth.) STREPTOMYCES (bacteria) / References: uk63052
#3: Chemical ChemComp-HQU / 3-HYDROXYQUINALDIC ACID


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 189.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO3
Details: QUINOMYCIN UK63052 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 HYDROXYQUINOXALINE ...Details: QUINOMYCIN UK63052 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 HYDROXYQUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: uk63052
Compound detailsQUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. ...QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, QUINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) HQU

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsSolvent system: D2O
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- RESTRAINED MOLECULAR DYNAMICS USING A ...Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 0.5 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 120 AND 180 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.023 0.024 0.024 0.026 BOND (ANG) 0.011 0.011 0.011 0.011 ANGLES (DEG) 3.616 3.657 3.700 3.725 IMPROPERS (DEG) 0.274 0.285 0.241 0.298
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 4 / Conformers submitted total number: 4

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