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- PDB-2mhv: Solution Structure of Penicillium Antifungal Protein PAF -

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Basic information

Entry
Database: PDB / ID: 2mhv
TitleSolution Structure of Penicillium Antifungal Protein PAF
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / penicillium / antifungal / basic / disulfide / stable / chrysogenum
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism
Similarity search - Function
Antifungal protein domain / Antifungal protein / Antifungal protein domain superfamily / Antifungal protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPenicillium chrysogenum (fungus)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsFizil, A. / Batta, G.
CitationJournal: Chemistry / Year: 2015
Title: "Invisible" Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations.
Authors: Fizil, A. / Gaspari, Z. / Barna, T. / Marx, F. / Batta, G.
History
DepositionDec 5, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Jun 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)6,2631
Polymers6,2631
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Antifungal protein


Mass: 6263.099 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: paf / Production host: Escherichia coli (E. coli) / References: UniProt: Q01701

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Re-refined structure of Penicillium Antifungal Protein (PAF).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D HNHA
11213D 1H-15N NOESY
11313D 1H-15N TOCSY
11413D (H)CCH-COSY
11513D 1H-13C NOESY
11612D 1H-1H NOESY

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Sample preparation

DetailsContents: 10 mM sodium phosphate, 40 mM sodium chloride, 1.7 mM [U-99% 13C; U-99% 15N] entity, 0.6 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphate-11
40 mMsodium chloride-21
1.7 mMentity-3[U-99% 13C; U-99% 15N]1
0.6 mMsodium azide-41
Sample conditionsIonic strength: 0.025 / pH: 6.0 / Pressure: ambient atm / 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
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Herrmann, Guntert and Wuthrichstructure solution
CYANA2.1Herrmann, Guntert and Wuthrichpeak picking
CYANA2.1Herrmann, Guntert and Wuthrichchemical shift assignment
CYANA2.1Keller and Wuthrichstructure solution
CYANA2.1Keller and Wuthrichpeak picking
CYANA2.1Keller and Wuthrichchemical shift assignment
TALOSTALOS+Cornilescu, Delaglio and Baxrefinement
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: using 7 cycles with 80 initial structures
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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