+Open data
-Basic information
Entry | Database: PDB / ID: 1o5p | ||||||
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Title | Solution Structure of holo-Neocarzinostatin | ||||||
Components | Neocarzinostatin | ||||||
Keywords | ANTIBIOTIC / PROTEIN-LIGAND COMPLEX / 7 STRANDED BETA BARREL / CROMOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces carzinostaticus (bacteria) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing with random array initial structures | ||||||
Authors | Takashima, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o5p.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1o5p.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 1o5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/1o5p ftp://data.pdbj.org/pub/pdb/validation_reports/o5/1o5p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-CHR / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | 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 ...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. |
-Sample preparation
Details | Contents: 2.5mM holo-Neocarzinostatin U-15N, 13C / Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 5.0 / Pressure: ambient / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software | Name: X-PLOR / Version: NIH 2.0.6 / Classification: refinement |
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Refinement | Method: distance geometry, simulated annealing with random array initial structures Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 16000 / Conformers submitted total number: 60 |