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- PDB-5oqs: Solution structure of antifungal protein NFAP -

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Basic information

Entry
Database: PDB / ID: 5oqs
TitleSolution structure of antifungal protein NFAP
ComponentsNFAP
KeywordsANTIFUNGAL PROTEIN / STRUCTURE FROM CYANA 2.1 / Solution structure / NFAP
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / Uncharacterized protein
Function and homology information
Biological speciesAspergillus fischeri NRRL 181 (mold)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsHajdu, D. / Czajlik, A. / Marx, F. / Galgoczy, L. / Batta, G.
Funding support Hungary, Austria, 3items
OrganizationGrant numberCountry
NKFIHANN 110821 Hungary
European UnionGINOP-2.3.2-15-2016-00008 Hungary
Austrian Science FundM1776-B20 Austria
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Solution structure and novel insights into phylogeny and mode of action of the Neosartorya (Aspergillus) fischeri antifungal protein (NFAP).
Authors: Hajdu, D. / Huber, A. / Czajlik, A. / Toth, L. / Kele, Z. / Kocsube, S. / Fizil, A. / Marx, F. / Galgoczy, L. / Batta, G.
History
DepositionAug 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 23, 2021Group: Data collection / Derived calculations / Category: pdbx_nmr_spectrometer / struct_conn
Item: _pdbx_nmr_spectrometer.field_strength / _struct_conn.pdbx_dist_value ..._pdbx_nmr_spectrometer.field_strength / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NFAP


Theoretical massNumber of molelcules
Total (without water)6,6401
Polymers6,6401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4600 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #9medoid

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Components

#1: Protein NFAP


Mass: 6639.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Food, canned fruit (apples) / Source: (gene. exp.) Aspergillus fischeri NRRL 181 (mold) / Gene: NFIA_112130 / Plasmid: pSK275nfappaf_signal / Production host: Penicillium chrysogenum (fungus) / Strain (production host): Wis. Q176 / References: UniProt: A1D8H8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H NOESY
121isotropic23D 1H-15N NOESY
232isotropic23D 1H-13C NOESY aliphatic
242isotropic12D 1H-15N HSQC
252isotropic12D 1H-13C HSQC
2132isotropic13D 1H-15N TOCSY
2122isotropic13D HNCA
2112isotropic13D HN(CA)CB
2142isotropic13D HNCO
2102isotropic13D HN(CO)CA
292isotropic13D HNHA
282isotropic13D HN(COCA)CB
272isotropic13D HN(CA)CO
161isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution120 mM [U-100% 2H] acetic acid, 1.1 mM [U-100% 15N] NFAP, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2Oshigemi sample tube, 275 ul volume15N_sample95% H2O/5% D2O
solution21 mM [U-100% 13C; U-100% 15N] NFAP, 20 mM [U-100% 2H] acetic acid, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2Oshigemi sample tube, 275 ul volume13C_15N_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMacetic acid[U-100% 2H]1
1.1 mMNFAP[U-100% 15N]1
95 %H2Onatural abundance1
5 %D2O[U-2H]1
1 mMNFAP[U-100% 13C; U-100% 15N]2
20 mMacetic acid[U-100% 2H]2
95 %H2Onatural abundance2
5 %D2O[U-2H]2
Sample conditions

Ionic strength: 0.007 M / Ionic strength err: 0.0007 / pH: 4.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 1

Conditions-IDLabel
1conditions_1
2conditions_2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II5001
Bruker AVANCE IIBrukerAVANCE II7002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.9.0Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
TALOS+Cornilescu, Delaglio and Baxrefinement
TopSpin3Bruker Biospinprocessing
Refinement
MethodSoftware ordinal
simulated annealing1
torsion angle dynamics2
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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