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- PDB-2nbf: Structure of calcium-bound form of Penicillium antifungal protein... -

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Basic information

Entry
Database: PDB / ID: 2nbf
TitleStructure of calcium-bound form of Penicillium antifungal protein (PAF)
ComponentsAntifungal proteinAntifungal protein family
KeywordsANTIFUNGAL PROTEIN / antifungal / PAF / calcium binding
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 / simulated annealing, torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsFizil, A. / Batta, G.
CitationJournal: To be Published
Title: Calcium binding and the role of aspartic acids in the antifungal function of PAF
Authors: Sonderegger, C. / Fizil, A. / Burtscher, L. / Komaromi, I. / Czajlik, A. / Munoz, A. / Hegedus, N. / Read, N. / Batta, G. / Marx, F.
History
DepositionFeb 4, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 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

Downloads & links

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Assembly

Deposited unit
A: Antifungal protein


Theoretical massNumber of molelcules
Total (without water)6,2631
Polymers6,2631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Antifungal protein / Antifungal protein family


Mass: 6263.099 Da / Num. of mol.: 1 / Fragment: UNP residue 38-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: paf / Production host: Penicillium chrysogenum (fungus) / References: UniProt: Q01701

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D 1H-15N NOESY
1513D 1H-15N TOCSY
1612D 1H-15N HSQC
1712D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-100% 15N] PAFD19S, 5 v/v [U-2H] D2O, 40 mM sodium chloride, 10 mM sodium phosphate, 0.04 % potassium phosphate, 10 mM Calcium ion, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMPAFD19S-1[U-100% 15N]1
5 v/vD2O-2[U-2H]1
40 mMsodium chloride-31
10 mMsodium phosphate-41
0.04 %potassium phosphate-51
10 mMCalcium ion-61
Sample conditionsIonic strength: 0.02 / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CYANA2.1Guntert, Braun and Wuthrichstructure solution
ATNOS-CANDIDHerrmann, Guntert and Wuthrichchemical shift assignment
ATNOS-CANDIDHerrmann, Guntert and Wuthrichpeak picking
ATNOS-CANDIDHerrmann, Guntert and Wuthrichstructure solution
CCPN_Analysis2.4CCPNchemical shift assignment
CYANArefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 808
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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