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- PDB-1rl5: NMR structure with tightly bound water molecule of cytotoxin I fr... -

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Basic information

Entry
Database: PDB / ID: 1rl5
TitleNMR structure with tightly bound water molecule of cytotoxin I from Naja oxiana in aqueous solution (major form)
ComponentsCytotoxin 1
KeywordsTOXIN / S-type cytotoxin / membrane perturbation / cis/trans isomerization / bound water
Function / homology
Function and homology information


other organism cell membrane / toxin activity / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Snake cytotoxin, cobra-type / Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesNaja oxiana (Central Asian cobra)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDubinnyi, M.A. / Pustovalova, Y.E. / Dubovskii, P.V. / Utkin, Y.N. / Arseniev, A.S.
CitationJournal: Biochem.J. / Year: 2005
Title: Interaction of three-finger toxins with phospholipid membranes: comparison of S- and P-type cytotoxins.
Authors: Dubovskii, P.V. / Lesovoy, D.M. / Dubinnyi, M.A. / Konshina, A.G. / Utkin, Y.N. / Efremov, R.G. / Arseniev, A.S.
History
DepositionNov 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytotoxin 1


Theoretical massNumber of molelcules
Total (without water)6,8311
Polymers6,8311
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytotoxin 1


Mass: 6831.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja oxiana (Central Asian cobra) / Secretion: venome / References: UniProt: P01451
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
162DQF-COSY
NMR detailsText: Cytotoxin I major and minor conformational states (in ratio of 6:1) in aqueous solution, corresponding to trans and cis val7-pro8 peptide bond conformations, were established via NMR spectra ...Text: Cytotoxin I major and minor conformational states (in ratio of 6:1) in aqueous solution, corresponding to trans and cis val7-pro8 peptide bond conformations, were established via NMR spectra analysis. Here is the obtained major structure of cytotoxin I. The presented at HETATM section HOH in each model are tightly bound water molecules (with longer than for bulk water lifetimes nearby protein), reaveled by NMR approach. The principle of apportionment of these water molecules differs from that in crystal structures, for which the water molecules being at the proximity to protein are indicated.

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Sample preparation

Details
Solution-IDContentsSolvent system
120mM Cytotoxin I, 50mM KCl, H2OKCl: 50mM, H2O
220mM Cytotoxin I, 50mM KCl, D2OKCl: 50mM, D2O
Sample conditionsIonic strength: 50 mM / pH: 6 / Pressure: normal / Temperature: 323 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1.acollection
XwinNMR3.1.aprocessing
XEASY1.2.11Bartels. C.data analysis
CYANA1.0.6Guntert, P.structure solution
NMRPipeApril 12, 2001Delagio, F.processing
ACME2001.085.20.47Delagio, F.data analysis
CYANA1.0.6Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 478 NOE-derived constraints, 202 angular constraints, 186 constraints for 31 hydrogen bonds, 24 constraints for 4 SS-bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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