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- PDB-1xj1: 3D solution structure of the C-terminal cysteine-rich domain of t... -
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Open data
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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 | ||||||
![]() | cysteine-rich omega-conotoxin homolog VHv1.1 | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics, simulated annealing protocols using CNS | ||||||
![]() | Einerwold, J. / Jaseja, J. / Hapner, K. / Webb, B. / Copie, V. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344.4 KB | Display | ![]() |
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PDB format | ![]() | 296.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 342.1 KB | Display | ![]() |
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Full document | ![]() | 482.3 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xi7C ![]() 1x17 C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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 |
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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 |
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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 |