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- PDB-1dey: NMR SOLUTION STRUCTURE OF CO(II)-BLEOMYCIN A2 -

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Basic information

Entry
Database: PDB / ID: 1dey
TitleNMR SOLUTION STRUCTURE OF CO(II)-BLEOMYCIN A2
Components
  • (0) x BLEOMYCIN A2
  • (1) x COBALT (II) ION
KeywordsANTIBIOTIC
Function / homologyBLEOMYCIN A2 / :
Function and homology information
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsLehmann, T.E. / Serrano, M.L. / Que Jr., L.
CitationJournal: Biochemistry / Year: 2000
Title: Coordination chemistry of co(II)-bleomycin: its investigation through NMR and molecular dynamics.
Authors: Lehmann, T.E. / Serrano, M.L. / Que Jr., L.
History
DepositionNov 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,4752
Polymers00
Non-polymers1,4752
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Chemical ChemComp-BLM / BLEOMYCIN A2 / N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE


Mass: 1416.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H85N17O21S3 / Comment: medication*YM
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-COSY, 2D-TOCSY, 2D-HMQC, T1 measument
2222D-COSY, 2D-TOCSY, 2D-HMQC, T1 measument
NMR detailsText: This structure was determined using standard 2D homonuclear techniques and T1 measuments

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Sample preparation

Details
Solution-IDContentsSolvent system
110mM Co(II)-BLM, 100% D2O, 50mM NaOD to adjust pH to 6.5100% D2O
210mM Co(II)-BLM, 90% H2O, 10% D2O, 50mM NaOH to adjust pH to 6.590% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 ambient 298 K
26.5 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXR500VarianVXR5005001
Varian VXR300VarianVXR3003002
Bruker AMX360BrukerAMX3603603

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Processing

NMR software
NameVersionDeveloperClassification
DISCOVER_397Biosym/MSIstructure solution
DISCOVER_397Biosym/MSIrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 31 T1-derived distance constraints
NMR ensembleConformers submitted total number: 1

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