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- PDB-6trm: Solution structure of the antifungal protein PAFC -

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Basic information

Entry
Database: PDB / ID: 6trm
TitleSolution structure of the antifungal protein PAFC
ComponentsPc21g12970 protein
KeywordsANTIMICROBIAL PROTEIN / SOLUTION STRUCTURE / DISULPHIDE PROTEIN / PAFC / STRUCTURE FROM CYANA 2.1
Function / homologyBubble protein / Bubble superfamily / Bubble protein / Pc21g12970 protein
Function and homology information
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCzajlik, A. / Holzknecht, J. / Marx, F. / Batta, G.
Funding support Hungary, Austria, 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
Austrian Science FundFWF I3132-B21 Austria
CitationJournal: Int J Mol Sci / Year: 2021
Title: Solution Structure, Dynamics, and New Antifungal Aspects of the Cysteine-Rich Miniprotein PAFC.
Authors: Czajlik, A. / Holzknecht, J. / Galgoczy, L. / Toth, L. / Poor, P. / Ordog, A. / Varadi, G. / Kuhbacher, A. / Borics, A. / Toth, G.K. / Marx, F. / Batta, G.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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
Revision 1.2Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.field_strength
Revision 1.3Jun 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: Pc21g12970 protein


Theoretical massNumber of molelcules
Total (without water)6,6391
Polymers6,6391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3740 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 Pc21g12970 protein


Mass: 6639.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium rubens Wisconsin 54-1255 (fungus)
Gene: Pc21g12970, PCH_Pc21g12970 / Plasmid: pSK275pafC
Production host: Penicillium rubens Wisconsin 54-1255 (fungus)
References: UniProt: B6HMF2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic12D 1H-15N HSQC
222isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-1H TOCSY
252isotropic13D 1H-15N NOESY
2112isotropic13D 1H-15N TOCSY
2102isotropic13D HNHA
292isotropic13D HNCA
282isotropic13D HN(CO)CA
272isotropic13D HN(CA)CB
262isotropic13D HN(COCA)CB
2132isotropic13D HNCO
2122isotropic13D HN(CA)CO
2142isotropic13D (H)CCH-TOCSY
2152isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution120 mM [U-100% 2H] acetic acid, 1.5 mM PAFC, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O5mm sample tube, 500 ul volumeunlabeled95% H2O/5% D2O
solution220 mM [U-100% 2H] acetic acid, 650 uM [U-100% 13C; U-100% 15N] PAFC, 95 % H2O, 5 % [U-2H] D2O, 95% H2O/5% D2O5mm sample tube, 440 ul volume13C_15N95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMacetic acid[U-100% 2H]1
1.5 mMPAFCnatural abundance1
95 %H2Onatural abundance1
5 %D2O[U-2H]1
20 mMacetic acid[U-100% 2H]2
650 uMPAFC[U-100% 13C; U-100% 15N]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
11
22

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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
TALOSNCornilescu, Delaglio and Baxrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpin3.1Bruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
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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