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- PDB-1s6w: Solution Structure of hybrid white striped bass hepcidin -

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Basic information

Entry
Database: PDB / ID: 1s6w
TitleSolution Structure of hybrid white striped bass hepcidin
ComponentsHepcidin
KeywordsANTIBIOTIC / two strand antiparalell beta sheet
Function / homologyHepcidin / Hepcidin / hormone activity / intracellular iron ion homeostasis / defense response to bacterium / extracellular region / Hepcidin
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsBabon, J.J. / Singh, S. / Pennington, M.W. / Norton, R.S. / Westerman, M.E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Bass hepcidin synthesis, solution structure, antimicrobial activities and synergism, and in vivo hepatic response to bacterial infections.
Authors: Lauth, X. / Babon, J.J. / Stannard, J.A. / Singh, S. / Nizet, V. / Carlberg, J.M. / Ostland, V.E. / Pennington, M.W. / Norton, R.S. / Westerman, M.E.
History
DepositionJan 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Oct 9, 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: Hepcidin


Theoretical massNumber of molelcules
Total (without water)2,2661
Polymers2,2661
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 / 100The submitted conformer models are the 20 structures with the lowest energy
RepresentativeModel #4closest to the average

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Components

#1: Protein/peptide Hepcidin


Mass: 2265.773 Da / Num. of mol.: 1 / Fragment: hepcidin, mature form (residues 65-85) / Source method: obtained synthetically
Details: the protein was chemically synthesized, the sequence of the protein occurs naturally in hybrid white striped bass
References: UniProt: P82951
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
242E-COSY
2522D NOESY
16113C-HSQC
NMR detailsText: this structure was determined using standard 2D homonuclear techniques and chemical shift data was obtained using standard 2D heteronuclear techniques performed at natural abundance isotope levels

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5mM hepcidin, 95% H2O, 5% D2O, pH=4.795% H2O/5% D2O
23.5mM hepcidin, 100% D2O, 10mM CD3COONa, pH=4.5100% D2O; 10mM CD3COONa pH=4.5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
104.71 atm298 K
210mM CD3COONa 4.51 atm298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR-NIH2.0.6C.D.Schwieters, J.J.Kuszewski, N.Tjandra and G.M.Clorestructure solution
NMRPipe1F.Delaglio, S.Grzesiek, G.W.Vuister, G. Zhu, J.Pfeifer and A.Baxdata analysis
XwinNMR3.5brukercollection
X-PLOR-NIH2.0.6C.D.Schwieters, J.J.Kuszewski, N.Tjandra and G.M.Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: the structures are based on 188 NOE-derived distance constraints, 238 dihedral angle restraints, 4 distance restraintsfrom hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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