+Open data
-Basic information
Entry | Database: PDB / ID: 5lue | |||||||||||||||||||||
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Title | Minor form of the recombinant cytotoxin-1 from N. oxiana | |||||||||||||||||||||
Components | VC-1=CYTOTOXIN | |||||||||||||||||||||
Keywords | TOXIN / cytolytic peptide / all-beta sheet protein / cobra venom / 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 / restrained Rosetta minimization | |||||||||||||||||||||
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. #1: Journal: To Be Published Title: Towards universal approach for bacterial production of three-finger Ly6/uPAR proteins: case study of Cytotoxin I from cobra N. oxiana Authors: Shulepko, M.A. / Lyukmanova, E.N. / Shenkarev, Z.O. / Dubovskii, P.V. / Astapova, M.V. / Feofanov, A.V. / Arseniev, A.S. / Utkin, Y.N. / Kirpichnikov, M.P. / Dolgikh, D.A. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lue.cif.gz | 382 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lue.ent.gz | 330.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/5lue ftp://data.pdbj.org/pub/pdb/validation_reports/lu/5lue | HTTPS FTP |
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-Related structure data
Related structure data | 5npnC 5t8aC 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 encoding 60 amino acid residues with additional ATG codon at the 5(prime)-end was constructed from six overlapping synthetic oligonucleotides using PCR Source: (gene. exp.) Naja oxiana (Central Asian cobra) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9PS33, UniProt: P01451*PLUS |
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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-1, 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: uniformly labeled 13C-15N recombinant toxin was dissolved in H2O/D2O(95:5 v/v) 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: identical to those used at the investigation of the native toxin (deposited under 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 | Method: restrained Rosetta minimization / Software ordinal: 4 Details: as in: J Am Chem Soc. 2014 Feb 5;136(5):1893-906. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. Mao B, Tejero R, Baker D, Montelione GT. | ||||||||||||||||||||||||
NMR representative | Selection criteria: quality score | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 |