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- PDB-7luw: Structural studies about ScnTx neurotoxin using Solution NMR 2D and 3D -

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Entry
Database: PDB / ID: 7luw
TitleStructural studies about ScnTx neurotoxin using Solution NMR 2D and 3D
ComponentsShort-chain neurotoxin
KeywordsNEUROPEPTIDE / toxins / neurotoxin / SCNTX
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Authorsdel Rio-Portilla, F. / Lopez-Giraldo, A.E.
CitationJournal: To Be Published
Title: The Three-Dimensional Structure of the Neurotoxin SCNTX
Authors: del Rio-Portilla, F. / Lopez-Giraldo, A.E.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain neurotoxin


Theoretical massNumber of molelcules
Total (without water)8,7111
Polymers8,7111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Short-chain neurotoxin


Mass: 8711.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H COSY
142isotropic13D 1H-15N NOESY
152isotropic13D 1H-15N TOCSY
182isotropic13D H(CCO)NH
172isotropic13D (H)CCH-TOCSY
162isotropic13D C(CO)NH
192isotropic13D HNCA
1122isotropic13D HN(CA)CB
1112isotropic13D HNCO
1102isotropic12D 1H-13C HSQC
1132isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM SCNTX NEUROTOXIN, 95% H2O/5% D2O1H95% H2O/5% D2O
solution20.7 mM [U-100% 13C; U-100% 15N, 1H] SCNTX NEUROTOXIN, 95% H2O/5% D2O1H, 15N, 13C95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSCNTX NEUROTOXINnatural abundance1
0.7 mMSCNTX NEUROTOXIN[U-100% 13C; U-100% 15N, 1H]2
Sample conditionsIonic strength: 0 Not defined / Label: 1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.5Keller and Wuthrichchemical shift assignment
NMRFAM-SPARKYWoonghee Lee, John L. Markley and John L. Markleychemical shift assignment
CARA1.5Keller and Wuthrichpeak picking
TALOSNCornilescu, Delaglio and Baxdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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