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- PDB-1la4: Solution Structure of SGTx1 -

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Basic information

Entry
Database: PDB / ID: 1la4
TitleSolution Structure of SGTx1
ComponentsSGTx1
KeywordsTOXIN / Triple-stranded antiparallel beta-sheet / inhibitory cystine knot / Peptide neurotoxin
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular space / Kappa-theraphotoxin-Scg1a
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLee, C.W. / Roh, S.H. / Kim, S. / Endoh, H. / Kodera, Y. / Maeda, T. / Swartz, K.J. / Kim, J.I.
CitationJournal: Biochemistry / Year: 2004
Title: Solution Structure and Functional Characterization of SGTx1, a Modifier of Kv2.1 Channel Gating
Authors: Lee, C.W. / Kim, S. / Roh, S.H. / Endoh, H. / Kodera, Y. / Maeda, T. / Kohno, T. / Wang, J.M. / Swartz, K.J. / Kim, J.I.
History
DepositionMar 28, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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: SGTx1


Theoretical massNumber of molelcules
Total (without water)3,7881
Polymers3,7881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #16closest to the average,lowest energy

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Components

#1: Protein/peptide SGTx1 / Voltage-gated potassium channel blocker


Mass: 3788.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence is chemically synthesized. / References: UniProt: P56855
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
121DQF-COSY
131PE-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM SGTx1; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.6Brukercollection
UXNMR2.6Brukerprocessing
X-PLOR3.851A.T.Brungerstructure solution
X-PLOR3.851A.T.Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 499 restraints, 449 are NOE-derived distance constraints, 27 dihedral angle ...Details: Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 499 restraints, 449 are NOE-derived distance constraints, 27 dihedral angle restraints,14 distance restraints from hydrogen bonds, and 9 distance restraints from disulfide bonds.
NMR representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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