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Basic information

Entry
Database: PDB / ID: 5kkm
TitleCon-Vc11-22
ComponentsO2_contryphan_Vc1 prepropeptide
KeywordsUNKNOWN FUNCTION / Single disulfide-directed beta hairpin / contryphan-Vc1 / stability / peptide scaffold
Function / homologyextracellular region / O2 contryphan Vc1
Function and homology information
Biological speciesConus victoriae (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsChittoor, B. / Krishnarjuna, B. / MacRaild, C.A. / Robinson, S.D.
CitationJournal: Biochemistry / Year: 2017
Title: The Single Disulfide-Directed beta-Hairpin Fold. Dynamics, Stability, and Engineering.
Authors: Chittoor, B. / Krishnarjuna, B. / Morales, R.A.V. / MacRaild, C.A. / Sadek, M. / Leung, E.W.W. / Robinson, S.D. / Pennington, M.W. / Norton, R.S.
History
DepositionJun 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O2_contryphan_Vc1 prepropeptide


Theoretical massNumber of molelcules
Total (without water)2,4851
Polymers2,4851
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2120 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide O2_contryphan_Vc1 prepropeptide


Mass: 2484.871 Da / Num. of mol.: 1 / Fragment: residues 68-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus victoriae (invertebrata) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: W4VSF6

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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 NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC
151isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 500 uM Con-Vc1R, 93% H2O/7% D2O / Details: 500uM / Label: Con-Vc1R / Solvent system: 93% H2O/7% D2O
SampleConc.: 500 uM / Component: Con-Vc1R / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: Condition_1 / pH: 4.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
Analysis2.1.5CCPNpeak picking
Analysis2.1.5CCPNchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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