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- PDB-2mn5: NMR structure of Copsin -

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Basic information

Entry
Database: PDB / ID: 2mn5
TitleNMR structure of Copsin
ComponentsCopsin
KeywordsANTIMICROBIAL PROTEIN / Antibiotic and Antimicrobial protein
Function / homologyDefensin A-like - #140 / Fungal defensin Copsin / Fungal defensin Copsin / Extracellular membrane protein, CFEM domain / CFEM domain / Defensin A-like / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsHofmann, D. / Wider, G. / Essig, A. / Aebi, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Copsin, a Novel Peptide-based Fungal Antibiotic Interfering with the Peptidoglycan Synthesis.
Authors: Essig, A. / Hofmann, D. / Munch, D. / Gayathri, S. / Kunzler, M. / Kallio, P.T. / Sahl, H.G. / Wider, G. / Schneider, T. / Aebi, M.
History
DepositionMar 28, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Database references
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_nmr_software ...entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copsin


Theoretical massNumber of molelcules
Total (without water)6,0851
Polymers6,0851
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Copsin


Mass: 6085.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Production host: Pichia pastoris (fungus) / References: UniProt: D6RKI7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-1H TOCSY
1422D DQF-COSY
1522D 1H-1H NOESY
1623D 1H-15N TOCSY
1723D HN(CO)CA
1823D 1H-15N NOESY
1923D 1H-13C NOESY
11012D 1H-1H NOESY
11113D HNCO
21222D 1H-15N HSQC
NMR detailsText: the structure calculation was performed using 2D and 3D noesy experiments, including hydrogen bonds determined by long range HNCO spectra

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate, 50 mM sodium chloride, 100% D2O100% D2O
220 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate-11
50 mMsodium chloride-21
20 mMsodium phosphate-32
50 mMsodium chloride-42
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
170 6.8 ambient 293 K
270 7.4 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntondata analysis
XEASY1.8.4Bartels et al.chemical shift assignment
XEASY1.8.4Bartels et al.peak picking
TopSpin3Bruker Biospincollection
TALOStalos+Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 823 / NOE intraresidue total count: 223 / NOE long range total count: 230 / NOE medium range total count: 126 / NOE sequential total count: 236
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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