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Yorodumi- PDB-1xj1: 3D solution structure of the C-terminal cysteine-rich domain of t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xj1 | ||||||
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Title | 3D solution structure of the C-terminal cysteine-rich domain of the VHv1.1 polydnaviral gene product | ||||||
Components | cysteine-rich omega-conotoxin homolog VHv1.1 | ||||||
Keywords | VIRAL PROTEIN / polydnavirus / cystine knot / cys-motif / beta-sheet structure / disulfide bonding patterns | ||||||
Function / homology | Cysteine rich domain, Polydnavirus / Viral cysteine rich / Omega-AgatoxinV - #20 / Omega-AgatoxinV / Few Secondary Structures / Irregular / Cysteine rich domain-containing protein Function and homology information | ||||||
Biological species | Campoletis sonorensis ichnovirus | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing protocols using CNS | ||||||
Authors | Einerwold, J. / Jaseja, J. / Hapner, K. / Webb, B. / Copie, V. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Solution structure of the carboxyl-terminal cysteine-rich domain of the VHv1.1 polydnaviral gene product: comparison with other cystine knot structural folds Authors: Einerwold, J. / Jaseja, J. / Hapner, K. / Webb, B. / Copie, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xj1.cif.gz | 344.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xj1.ent.gz | 296.6 KB | Display | PDB format |
PDBx/mmJSON format | 1xj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/1xj1 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/1xj1 | HTTPS FTP |
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-Related structure data
Related structure data | 1xi7C 1x17 C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6521.473 Da / Num. of mol.: 1 / Fragment: C-terminal cys-motif Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campoletis sonorensis ichnovirus / Genus: Ichnovirus / Gene: pVX900 / Plasmid: pET-32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89632 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This ensemble of NMR structures was determined using standard 2D 1H homonuclear NMR techniques |
-Sample preparation
Details | Contents: 1mM C-term VHv1.1, 25mM sodium phosphate, 100mM NaCl, 1mM EDTA, 0.01% sodium azide Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, simulated annealing protocols using CNS Software ordinal: 1 Details: The structures are based on 280 NOE-derived interproton distance constraints, 24 distance restraints from 12 hydrogen bonds | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 25 / Conformers submitted total number: 25 |