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Yorodumi- PDB-1r9u: Refined structure of peptaibol zervamicin IIB in methanol solutio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r9u | ||||||
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Title | Refined structure of peptaibol zervamicin IIB in methanol solution from trans-hydrogen bond J couplings | ||||||
Components | ZERVAMICIN IIB | ||||||
Keywords | ANTIBIOTIC / ZREVAMICIN / BIFURCATED HYDROGEN BOND / PEPTAIBOL / ANTIBACTERIAL / ANTIFUNGAL / BENT HELIX | ||||||
Function / homology | Zervamicin IIB / : Function and homology information | ||||||
Biological species | EMERICELLOPSIS SALMOSYNNEMATA (fungus) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, ENERGY MINIMISATION | ||||||
Authors | Shenkarev, Z.O. / Balashova, T.A. / Yakimenko, Z.A. / Ovchinnikova, T.V. / Arseniev, A.S. | ||||||
Citation | Journal: J.Pept.Sci. / Year: 2003 Title: Biosynthetic Uniform 13C,15N-Labelling of Zervamicin Iib. Complete 13C and 15N NMR Assignment. Authors: Ovchinnikova, T.V. / Shenkarev, Z.O. / Yakimenko, Z.A. / Svishcheva, N.V. / Tagaev, A.A. / Skladnev, D.A. / Arseniev, A.S. #1: Journal: FEBS Lett. / Year: 2000 Title: NMR Structure of the Channel-Former Zervamicin Iib in Isotropic Solvents Authors: Balashova, T.A. / Shenkarev, Z.O. / Tagaev, A.A. / Ovchinnikova, T.V. / Raap, J. / Arseniev, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r9u.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r9u.ent.gz | 87.9 KB | Display | PDB format |
PDBx/mmJSON format | 1r9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r9u_validation.pdf.gz | 353.7 KB | Display | wwPDB validaton report |
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Full document | 1r9u_full_validation.pdf.gz | 390.5 KB | Display | |
Data in XML | 1r9u_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 1r9u_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/1r9u ftp://data.pdbj.org/pub/pdb/validation_reports/r9/1r9u | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: LONG RANGE 2D-HNCO |
NMR details | Text: THIS STRUCTURE IS A REFINED STRUCTURE OF PREVIOUS DEPOSITION (1DLZ) ON THE BASIS OF HYDROGEN BOND RESTRAINTS, DETERMINED EXPERIMENTALY. INCLUDING RESTRAINTS FOR OBSERVED BIFURCATED HYDROGEN BOND. |
-Sample preparation
Details | Contents: 4MM U-15N-13C ZRV-IIB, METHANOL (CD3OH) PH 6.2 |
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Sample conditions | Ionic strength: 0 / pH: 6.2 / Pressure: 1 atm / Temperature: 305 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING, TORSION ANGLE DYNAMICS, ENERGY MINIMISATION Software ordinal: 1 Details: STRUCTURE WAS REFINED USING ADDITIONAL 22/22 (UPPER/LOWER) RESTRAINTS FOR HYDROGEN BONDS. REFINEMENT WAS DONE IN ECEPP/2 FORCE FIELD USING IMPLICIT SOLVENT MODEL | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION Conformers calculated total number: 1000 / Conformers submitted total number: 24 |