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- PDB-2da8: SOLUTION STRUCTURE OF A COMPLEX BETWEEN (N-MECYS3,N-MECYS7)TANDEM... -

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Basic information

Entry
Database: PDB / ID: 2da8
TitleSOLUTION STRUCTURE OF A COMPLEX BETWEEN (N-MECYS3,N-MECYS7)TANDEM AND (D(GATATC))2
Components
  • CysMeTANDEM quinoxaline antibiotic
  • DNA (5'-D(*GP*AP*TP*AP*TP*C)-3')
KeywordsDNA/ANTIBIOTIC / BISINTERCALATOR / DEPSIPEPTIDE / QUINOXALINE / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX
Function / homology2-CARBOXYQUINOXALINE / : / DNA
Function and homology information
Biological speciesSTREPTOMYCINEAE (bacteria)
MethodSOLUTION NMR / ENERGY MINIMIZATION, RESTRAINED MOLECULAR DYNAMICS, NOE BASED RELAXATION REFINEMENT
AuthorsAddess, K.J. / Sinsheimer, J.S. / Feigon, J.
CitationJournal: Biochemistry / Year: 1993
Title: Solution Structure of a Complex between [N-Mecys3,N-Mecys7]Tandem and [D(Gatatc)]2.
Authors: Addess, K.J. / Sinsheimer, J.S. / Feigon, J.
History
DepositionApr 9, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 1.4Nov 1, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly / pdbx_validate_polymer_linkage
Item: _pdbx_database_status.process_site / _pdbx_struct_assembly.method_details
Revision 1.5Aug 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CysMeTANDEM quinoxaline antibiotic
C: DNA (5'-D(*GP*AP*TP*AP*TP*C)-3')
D: DNA (5'-D(*GP*AP*TP*AP*TP*C)-3')
A: 2-CARBOXYQUINOXALINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7325
Polymers4,3833
Non-polymers3482
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-8 kcal/mol
Surface area3330 Å2
MethodPISA
Atom site foot note1: RESIDUES SER A 1 AND SER B 1 ARE D-AMINO ACIDS.
2: ALA A 2 - CYS A 3 MODEL 1 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ALA B 2 - CYS B 3 MODEL 1 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: ALA A 2 - CYS A 3 MODEL 2 OMEGA = 0.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: ALA A 2 - CYS A 3 MODEL 3 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: ALA B 2 - CYS B 3 MODEL 3 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: ALA A 2 - CYS A 3 MODEL 4 OMEGA =359.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: ALA B 2 - CYS B 3 MODEL 4 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: ALA A 2 - CYS A 3 MODEL 5 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: ALA B 2 - CYS B 3 MODEL 5 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: ALA A 2 - CYS A 3 MODEL 6 OMEGA = 0.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: ALA A 2 - CYS A 3 MODEL 7 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: ALA A 2 - CYS A 3 MODEL 8 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 8all calculated structures submitted
Representative

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Components

#1: Protein/peptide CysMeTANDEM quinoxaline antibiotic


Mass: 766.928 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Details: VALINE AT POSITIONS 4 AND 8 / Source: (synth.) STREPTOMYCINEAE (bacteria) / References: NOR: NOR01129
#2: DNA chain DNA (5'-D(*GP*AP*TP*AP*TP*C)-3')


Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-QUI / 2-CARBOXYQUINOXALINE


Mass: 174.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: FOR DISTANCE GEOMETRY, FULL STRUCTURE EMBEDS WERE DONE USING THE PROGRAM DSPACE (HARE RESEARCH, INC.) AND SUBSTRUCTURE EMBEDS WERE DONE USING X-PLOR (A. T. BRUNGER, YALE UNIVERSITY). ALL ...Text: FOR DISTANCE GEOMETRY, FULL STRUCTURE EMBEDS WERE DONE USING THE PROGRAM DSPACE (HARE RESEARCH, INC.) AND SUBSTRUCTURE EMBEDS WERE DONE USING X-PLOR (A. T. BRUNGER, YALE UNIVERSITY). ALL REFINEMENT STEPS WERE DONE USING X-PLOR.

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
DSPACEstructure solution
RefinementMethod: ENERGY MINIMIZATION, RESTRAINED MOLECULAR DYNAMICS, NOE BASED RELAXATION REFINEMENT
Software ordinal: 1
Details: EIGHT STRUCTURES WERE GENERATED BY DISTANCE GEOMETRY. TWO DIMENSIONAL DERIVED NOE AND DIHEDRAL BOND ANGLE CONSTRAINTS WERE USED THROUGHOUT ALL STAGES OF THE STRUCTURE CALCULATIONS. AVERAGE R ...Details: EIGHT STRUCTURES WERE GENERATED BY DISTANCE GEOMETRY. TWO DIMENSIONAL DERIVED NOE AND DIHEDRAL BOND ANGLE CONSTRAINTS WERE USED THROUGHOUT ALL STAGES OF THE STRUCTURE CALCULATIONS. AVERAGE R VALUE FOR 8 STRUCTURES 0.21
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 8 / Conformers submitted total number: 8
NMR ensemble rmsAtom type: all heavy atoms / Distance rms dev: 1.1 Å

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