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- PDB-7pgd: PAF in 50 v/v % DMSO-water solution -

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Basic information

Entry
Database: PDB / ID: 7pgd
TitlePAF in 50 v/v % DMSO-water solution
ComponentsPc24g00380 protein
KeywordsANTIMICROBIAL PROTEIN / DISULPHIDE PROTEIN / PAF / SOLUTION STRUCTURE / STRUCTURE FROM CYANA 2.1
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / Pc24g00380 protein
Function and homology information
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodSOLUTION NMR / simulated annealing / distance geometry
AuthorsCzajlik, A. / Batta, G.
Funding support Hungary, 3items
OrganizationGrant numberCountry
European Regional Development FundGINOP-2.3.2-15-2016-00008 Hungary
European Regional Development FundGINOP-2.3.3-15-2016-00004 Hungary
National Research Development and Innovation Office (NKFIH)K119509 Hungary
CitationJournal: Int J Mol Sci / Year: 2023
Title: DMSO-Induced Unfolding of the Antifungal Disulfide Protein PAF and Its Inactive Variant: A Combined NMR and DSC Study.
Authors: Czajlik, A. / Batta, A. / Kerner, K. / Fizil, A. / Hajdu, D. / Raics, M. / Kover, K.E. / Batta, G.
History
DepositionAug 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pc24g00380 protein


Theoretical massNumber of molelcules
Total (without water)6,2631
Polymers6,2631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4070 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Pc24g00380 protein


Mass: 6263.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Penicillium rubens Wisconsin 54-1255 (fungus)
References: UniProt: B6HWK0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-1H TOCSY
141isotropic13D HNHA
151isotropic13D HNHB
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution
Contents: 20 mM [U-100% 2H] acetic acid, 50 % v/v H2O, 50 % v/v [U-2H] DMSO, 1.7 mM [U-100% 15N] PAF, 50% H2O/50% DMSO
Details: 5 mm sample tube, 500 ul volume / Label: 15N_sample / Solvent system: 50% H2O/50% DMSO
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMacetic acid[U-100% 2H]1
50 % v/vH2Onatural abundance1
50 % v/vDMSO[U-2H]1
1.7 mMPAF[U-100% 15N]1
Sample conditionsIonic strength: 0.007 M / Ionic strength err: 0.0007 / Label: conditions_1 / pH: 4.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 310 K / Temperature err: 1

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Refinement
MethodSoftware ordinal
simulated annealing4
distance geometry5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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