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- PDB-2nc2: Structure, Dynamics and functional Aspects of the antifungal prot... -

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Basic information

Entry
Database: PDB / ID: 2nc2
TitleStructure, Dynamics and functional Aspects of the antifungal protein sfPAFB
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / disulfide / short form / PAF / AFP / NFAP
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / extracellular region / Antifungal protein
Function and homology information
Biological speciesPenicillium chrysogenum (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsBatta, G. / Fizil, A. / Hajdu, D.
CitationJournal: Sci Rep / Year: 2018
Title: New Antimicrobial Potential and Structural Properties of PAFB: A Cationic, Cysteine-Rich Protein from Penicillium chrysogenum Q176.
Authors: Huber, A. / Hajdu, D. / Bratschun-Khan, D. / Gaspari, Z. / Varbanov, M. / Philippot, S. / Fizil, A. / Czajlik, A. / Kele, Z. / Sonderegger, C. / Galgoczy, L. / Bodor, A. / Marx, F. / Batta, G.
History
DepositionMar 17, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifungal protein


Theoretical massNumber of molelcules
Total (without water)6,3161
Polymers6,3161
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Antifungal protein


Mass: 6316.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Strain: Q176 / Gene: afp, pafB / Production host: Penicillium chrysogenum (fungus) / Strain (production host): Q176 Delta-paf / References: UniProt: D0EXD3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: two residues shorter sequence at the N terminus if compared to "pgAFP" or "PAFB"
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D HNHA
11013D HN(COCA)CB
11112D 1H-1H NOESY
11213D 1H-15N NOESY
11313D 1H-15N TOCSY
11413D 1H-13C NOESY
11513D (H)CCH-COSY
11612D 1H-13C HSQC aliphatic
1171(HB)CB(CGCD)HD
11822D 1H-15N HSQC
11923D 1H-13C NOESY
12023D 1H-15N NOESY
12122D 1H-13C HSQC
12222D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.65 mM [U-100% 13C; U-100% 15N] protein, 20 mM [U-100% 2H] acetic acid, 95% H2O/5% D2O95% H2O/5% D2O
21 mM protein, 20 mM [U-2H] acetic acid, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.65 mMentity-1[U-100% 13C; U-100% 15N]1
20 mMacetic acid-2[U-100% 2H]1
1 mMentity-32
20 mMacetic acid-4[U-2H]2
Sample conditionsIonic strength: 7.5 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1; 3.0Bruker Biospincollection
TopSpin2.1; 3.0Bruker Biospinprocessing
CARA8.4Keller and Wuthrichpeak picking
CARA8.4Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ATNOSHerrmann, Guntert and Wuthrichpeak picking
CANDIDHerrmann, Guntert and Wuthrichchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxrefinement
CYANArefinement
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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