+Open data
-Basic information
Entry | Database: PDB / ID: 5t8a | |||||||||||||||||||||
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Title | Recombinant cytotoxin-I from the venom of cobra N. oxiana | |||||||||||||||||||||
Components | Cytotoxin 1 | |||||||||||||||||||||
Keywords | TOXIN / cytolytic peptide / all-beta sheet protein / recombinant production / Structure from MOLMOL | |||||||||||||||||||||
Function / homology | Function and homology information other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Naja oxiana (Central Asian cobra) | |||||||||||||||||||||
Method | SOLUTION NMR / simulated annealing / restrained Rosetta protocol | |||||||||||||||||||||
Authors | Dubovskii, P.V. / Dubinnyi, M.A. / Shulepko, M.A. / Lyukmanova, E.N. / Dolgikh, D.A. / Kirpichnikov, M.P. / Efremov, R.G. | |||||||||||||||||||||
Funding support | Russian Federation, 6items
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Citation | Journal: Biochemistry / Year: 2017 Title: Structural and Dynamic "Portraits" of Recombinant and Native Cytotoxin I from Naja oxiana: How Close Are They? Authors: Dubovskii, P.V. / Dubinnyi, M.A. / Konshina, A.G. / Kazakova, E.D. / Sorokoumova, G.M. / Ilyasova, T.M. / Shulepko, M.A. / Chertkova, R.V. / Lyukmanova, E.N. / Dolgikh, D.A. / Arseniev, A.S. / Efremov, R.G. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t8a.cif.gz | 373.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t8a.ent.gz | 323.4 KB | Display | PDB format |
PDBx/mmJSON format | 5t8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t8a_validation.pdf.gz | 389.2 KB | Display | wwPDB validaton report |
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Full document | 5t8a_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 5t8a_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5t8a_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8a ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8a | HTTPS FTP |
-Related structure data
Related structure data | 5lueC 5npnC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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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: 6962.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: the toxin gene with additional ATG codon at the 5prime-end was constructed from six overlapping synthetic oligonucleotides using PCR Source: (gene. exp.) Naja oxiana (Central Asian cobra) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01451 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1 mM U-99% 13C; U-99% 15N recombinant cytotoxin-I, 95 v/v non-labeled H2O, 5 v/v 99.9% 2H D2O, 3 uM non-labeled NaOH, 1 uM non-labeled HCl, 95% H2O/5% D2O Details: the double-labeled (13C-15N) recombinant toxin was dissolved in H2O/D2O (95/5) mixture and pH was adjusted with small additions of concentrated NaOH/HCl solutions Label: 13C-15N sample / Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Details: the conditions were chosen to match those used for the investigation of the native variant of this toxin (deposited under PDB code of 1RL5) Ionic strength: 0 Not defined / Ionic strength err: 0.1 / Label: conditions_1 / pH: 6.5 / PH err: 0.1 / Pressure: 101325 Pa / Pressure err: 100 / Temperature: 303 K / Temperature err: 0.2 |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement |
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NMR representative | Selection criteria: quality score | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 |