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- PDB-1x5v: NMR Structure of PcFK1 -

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Basic information

Entry
Database: PDB / ID: 1x5v
TitleNMR Structure of PcFK1
ComponentsPcFK1
KeywordsTOXIN / Inhibitory Cystine Knot
Function / homologytoxin activity / extracellular region / U1-theraphotoxin-Pc1a
Function and homology information
Biological speciesPsalmopoeus cambridgei (Trinidad chevron tarantula)
MethodSOLUTION NMR / molecular dynamics based simulated annealing
AuthorsPimentel, C. / Choi, S.J. / Chagot, B. / Guette, C. / Camadro, J.M. / Darbon, H.
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure of PcFK1, a spider peptide active against Plasmodium falciparum
Authors: Pimentel, C. / Choi, S.J. / Chagot, B. / Guette, C. / Camadro, J.M. / Darbon, H.
History
DepositionMay 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PcFK1


Theoretical massNumber of molelcules
Total (without water)3,7121
Polymers3,7121
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)25 / 100structures with the lowest energy, structures with the least restraint violations
Representative

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Components

#1: Protein/peptide PcFK1


Mass: 3712.397 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psalmopoeus cambridgei (Trinidad chevron tarantula)
Production host: Escherichia coli (E. coli) / References: UniProt: P0C201

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
2312D NOESY
241DQF-COSY
2512D TOCSY
2612D NOESY

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Sample preparation

DetailsContents: 1mM / Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13 1 atm290 K
23 1 atm300 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker biospinprocessing
ARIA1.2Jens Lingestructure solution
ARIA1.2Jens Lingerefinement
RefinementMethod: molecular dynamics based simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 25

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