+Open data
-Basic information
Entry | Database: PDB / ID: 2mj4 | ||||||
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Title | Neurotoxin II from snake venom Naja Oxiana in solution | ||||||
Components | Short neurotoxin 1 | ||||||
Keywords | TOXIN / 13C relaxation / side chain dynamics / molecular dynamics / molecular mechanics force fields / optimization | ||||||
Function / homology | Function and homology information acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Naja oxiana (Central Asian cobra) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | fewest violations, model1 | ||||||
Authors | Lesovoy, D.M. / Nolde, S.B. / Bocharov, E.V. / Lyukmanova, E.N. / Arseniev, A.S. | ||||||
Citation | Journal: To be Published Title: An NMR-based approach for validation of protein side-chains dynamics in silico Authors: Lesovoy, D.M. / Nolde, S.B. / Bocharov, E.V. / Lyukmanova, E.N. / 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 | 2mj4.cif.gz | 357 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mj4.ent.gz | 310.4 KB | Display | PDB format |
PDBx/mmJSON format | 2mj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mj4_validation.pdf.gz | 398.5 KB | Display | wwPDB validaton report |
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Full document | 2mj4_full_validation.pdf.gz | 497.6 KB | Display | |
Data in XML | 2mj4_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 2mj4_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/2mj4 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/2mj4 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6895.784 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naja oxiana (Central Asian cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: P01427 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Side chains dynamics from 13CH, 13CH2, 13CH3, 15NH, and 15NH2 NMR relaxation: R1, R2, NOE, dipole-dipole cross-correlation contribution to R1 and R2. Simulated NMR parameters from molecular dynamics trajectory. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 5.0 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The 1H-1H NOE amplitudes should be treated only according to the flexibility of the corresponding backbone or side chain groups: derived from the heteronuclear NOE, R1, R2, 1chch(dipolar ...Details: The 1H-1H NOE amplitudes should be treated only according to the flexibility of the corresponding backbone or side chain groups: derived from the heteronuclear NOE, R1, R2, 1chch(dipolar cross-correlation contribution to R1), 2chch(dipolar cross-correlation contribution to R2), and 3J scalar coupling constant values. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |