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- PDB-7l2g: NMR solution structure of Nak1 from the Necator americanus hookworm -

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Basic information

Entry
Database: PDB / ID: 7l2g
TitleNMR solution structure of Nak1 from the Necator americanus hookworm
ComponentsShTK domain protein
KeywordsIMMUNE SYSTEM
Function / homologyShK domain-like / ShKT domain / ShKT domain profile. / ShTK domain protein
Function and homology information
Biological speciesNecator americanus (New World hookworm)
MethodSOLUTION NMR / simulated annealing
AuthorsSmallwood, T.B. / Rosengren, K.J. / Clark, R.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT100100476 Australia
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Synthetic hookworm-derived peptides are potent modulators of primary human immune cell function that protect against experimental colitis in vivo.
Authors: Smallwood, T.B. / Navarro, S. / Cristofori-Armstrong, B. / Watkins, T.S. / Tungatt, K. / Ryan, R.Y.M. / Haigh, O.L. / Lutzky, V.P. / Mulvenna, J.P. / Rosengren, K.J. / Loukas, A. / Miles, J.J. / Clark, R.J.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ShTK domain protein


Theoretical massNumber of molelcules
Total (without water)4,3771
Polymers4,3771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ShTK domain protein


Mass: 4377.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Necator americanus (New World hookworm) / References: UniProt: W2TBE5

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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-13C HSQC
141isotropic12D DQF-COSY
151isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution / Contents: 1 mg/mL Nak1, 90% H2O/10% D2O / Label: Nak1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mg/mL / Component: Nak1 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: Conditions_1 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 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
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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