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- PDB-1o5p: Solution Structure of holo-Neocarzinostatin -

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Basic information

Entry
Database: PDB / ID: 1o5p
TitleSolution Structure of holo-Neocarzinostatin
ComponentsNeocarzinostatin
KeywordsANTIBIOTIC / PROTEIN-LIGAND COMPLEX / 7 STRANDED BETA BARREL / CROMOPROTEIN
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
NEOCARZINOSTATIN-CHROMOPHORE / Neocarzinostatin
Similarity search - Component
Biological speciesStreptomyces carzinostaticus (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing with random array initial structures
AuthorsTakashima, H. / Ishino, T. / Yoshida, T. / Hasuda, K. / Ohkubo, T. / Kobayashi, Y.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Solution NMR Structure Investigation for Releasing Mechanism of Neocarzinostatin Chromophore from the Holoprotein
Authors: Takashima, H. / Yoshida, T. / Ishino, T. / Hasuda, K. / Ohkubo, T. / Kobayashi, Y.
#1: Journal: J.Am.Chem.Soc. / Year: 2004
Title: Distributed Computing and NMR Constraint-Based High-Resolution Structure Determination: Applied for Bioactive Peptide Endothelin-1 To Determine C-Terminal Folding.
Authors: Takashima, H. / Mimura, N. / Ohkubo, T. / Yoshida, T. / Tamaoki, H. / Kobayashi, Y.
History
DepositionOct 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neocarzinostatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7602
Polymers11,1001
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)60 / 16000structures with the lowest energy
RepresentativeModel #60lowest energy

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Components

#1: Protein Neocarzinostatin / NCS / Mitomalcin / MMC


Mass: 11100.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Protein was isotope labeled by pre-enriched chlorella as amino acide source.
Source: (natural) Streptomyces carzinostaticus (bacteria) / References: UniProt: P0A3R9
#2: Chemical ChemComp-CHR / NEOCARZINOSTATIN-CHROMOPHORE / NCS-CHROMOPHORE


Mass: 659.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H33NO12
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY
NMR detailsText: Based on distributed computing (SUN GRID engine), the structure calculation explored conformational space comprehensively by using a huge number of initial structures to increase structure ...Text: Based on distributed computing (SUN GRID engine), the structure calculation explored conformational space comprehensively by using a huge number of initial structures to increase structure precision and convergence.

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Sample preparation

DetailsContents: 2.5mM holo-Neocarzinostatin U-15N, 13C / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY7501
Bruker AMXBrukerAMX6002

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Processing

NMR softwareName: X-PLOR / Version: NIH 2.0.6 / Classification: refinement
RefinementMethod: distance geometry, simulated annealing with random array initial structures
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 16000 / Conformers submitted total number: 60

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