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- PDB-1qms: Head-to-Tail Dimer of Calicheamicin gamma-1-I Oligosaccharide Bou... -

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Basic information

Entry
Database: PDB / ID: 1qms
TitleHead-to-Tail Dimer of Calicheamicin gamma-1-I Oligosaccharide Bound to DNA Duplex, NMR, 9 Structures
Components
  • DNA (5'-D(*GP*CP*AP*CP*CP*TP*TP*CP*CP*TP*GP*C)-3')
  • DNA (5'-D(*GP*CP*AP*GP*GP*AP*AP*GP*GP*TP*GP*C)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID/CALICHEAMICIN / CALICHEAMICIN / HEAD-TO-TAIL DIMER / MINOR GROOVE BINDING / ANTITUMOR AGENT / LIGAND-DNA COMPLEX / DEOXYRIBONUCLEIC ACID
Function / homologyCALICHEAMICIN GAMMA-1-OLIGOSACCHARIDE / N-BUTANE / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsBifulco, G. / Galeone, A. / Nicolaou, K.C. / Chazin, W.J. / Gomez-Paloma, L.
CitationJournal: J.Am.Chem.Soc. / Year: 1998
Title: Solution Structure of the Complex between the Head-to-Tail Dimer of Calicheamicin Gamma-1-I Oligosaccharide and a DNA Duplex Containing D(ACCT) and D(TCCT) High-Affinity Binding Sites
Authors: Bifulco, G. / Galeone, A. / Nicolaou, K.C. / Chazin, W.J. / Gomez-Paloma, L.
History
DepositionOct 6, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 1999Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Derived calculations / Version format compliance
Revision 1.2Mar 27, 2013Group: Derived calculations / Non-polymer description
Revision 1.3Mar 7, 2018Group: Database references / Source and taxonomy / Category: citation / pdbx_entity_src_syn
Item: _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4May 8, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_nmr_software / pdbx_seq_map_depositor_info ...pdbx_nmr_software / pdbx_seq_map_depositor_info / struct_conn / struct_ref_seq
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod ..._pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_end
Revision 1.5May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,3395
Polymers7,3272
Non-polymers2,0123
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 20LOWEST RESTRAINT VIOLATION
Representative

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Components

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


Mass: 3574.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*AP*GP*GP*AP*AP*GP*GP*TP*GP*C)-3')


Mass: 3752.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: COMPLEXED WITH CALICHEAMICIN HEAD-TO-TAIL DIMER / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CCI / CALICHEAMICIN GAMMA-1-OLIGOSACCHARIDE


Mass: 976.864 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C38H61IN2O17S
#4: Chemical ChemComp-NBU / N-BUTANE


Mass: 58.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
1412Q
151PE-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H NMR DATA

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Sample preparation

DetailsContents: 5% D2O/95% H2O
Sample conditionsIonic strength: 0.01 M SODIUM PHOSPHATE BUFFER, 0.01 M SODIUM CHLORIDE, O.0001 M EDTA
pH: 7.0 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, SEIBEL,SINGH,WEINER,KOLLMANrefinement
Amber4.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST RESTRAINT VIOLATION / Conformers calculated total number: 20 / Conformers submitted total number: 9

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