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- PDB-1hzl: SOLUTION STRUCTURES OF C-1027 APOPROTEIN AND ITS COMPLEX WITH THE... -

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Basic information

Entry
Database: PDB / ID: 1hzl
TitleSOLUTION STRUCTURES OF C-1027 APOPROTEIN AND ITS COMPLEX WITH THE AROMATIZED CHROMOPHORE
ComponentsC-1027 APOPROTEIN
KeywordsANTIBIOTIC / chromoprotein / C-1027 / apoprotein / aromatized chromophore
Function / homology
Function and homology information


defense response to bacterium / DNA binding
Similarity search - Function
Neocarzinostatin-like / Neocarzinostatin family / Neocarzinostatin family / Neocarzinostatin-like / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
C-1027 AROMATIZED CHROMOPHORE / Antitumor antibiotic C-1027 apoprotein
Similarity search - Component
Biological speciesStreptomyces globisporus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTanaka, T. / Fukuda-Ishisaka, S. / Hirama, M. / Otani, T.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structures of C-1027 apoprotein and its complex with the aromatized chromophore.
Authors: Tanaka, T. / Fukuda-Ishisaka, S. / Hirama, M. / Otani, T.
History
DepositionJan 25, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 5, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_planes / pdbx_validate_torsion
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.conformer_id / _pdbx_validate_planes.rmsd / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Revision 2.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-1027 APOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3522
Polymers10,5041
Non-polymers8471
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1030 Å2
ΔGint-12 kcal/mol
Surface area5570 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein C-1027 APOPROTEIN / ANTITUMOR ANTIBIOTIC C-1027 APOPROTEIN


Mass: 10504.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces globisporus (bacteria) / Strain: C-1027 / References: UniProt: Q06110
#2: Chemical ChemComp-ROM / C-1027 AROMATIZED CHROMOPHORE


Mass: 847.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H45ClN3O13

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
132COSY
242HOHAHA
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
1Sample 1: 8.3-8.6mM C-1027 apoprotein complexed with the aromatized chromophore; 99.996% D2O; Sample 2: 8.3-8.6mM C-1027 apoprotein complexed with the aromatized chromophore; 90% H2O, 10% D2O99.996% D2O; 90% H2O, 10% D2O
28.3-8.6mM C-1027 apoprotein complexed with the aromatized chromophore; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionspH: 5.0 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM / Manufacturer: Bruker / Model: AM / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brunger, A.T.structure solution
X-PLOR3.1Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1539 restraints: 1378 NOE-derived distance restraints, 95 dihedral angle restraints, 60 distance restraints from hydrogen bonds, and 6 distance ...Details: The structures are based on a total of 1539 restraints: 1378 NOE-derived distance restraints, 95 dihedral angle restraints, 60 distance restraints from hydrogen bonds, and 6 distance restraints from disulfide bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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