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- PDB-2bic: The solution structure of the recombinant elicitor protein PcF fr... -

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Basic information

Entry
Database: PDB / ID: 2bic
TitleThe solution structure of the recombinant elicitor protein PcF from the oomycete pathogen P. cactorum
ComponentsPHYTOTOXIC PROTEIN PCF
KeywordsTOXIN / PLANT PATHOGEN / PHYTOPHTHORA CACTORUM FRAGARIA PROTEIN / OOMYCETE PLANT PATHOGEN / ELICITIN FAMILY
Function / homologyHelix Hairpins - #540 / Phytotoxin, PcF / Phytotoxin PcF protein / Helix Hairpins / Helix non-globular / Special / Phytotoxic protein PcF
Function and homology information
Biological speciesPHYTOPHTHORA CACTORUM (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsNicastro, G. / Orsomando, G. / Desario, F. / Ferrari, E. / Manconi, L. / Spisni, A. / Ruggieri, S.
Citation
Journal: Protein Sci. / Year: 2009
Title: Solution Structure of the Phytotoxic Protein Pcf: The First Characterized Member of the Phytophthora Pcf Toxin Family.
Authors: Nicastro, G. / Orsomando, G. / Ferrari, E. / Manconi, L. / Desario, F. / Amici, A. / Naso, A. / Carpaneto, A. / Pertinhez, T.A. / Ruggieri, S. / Spisni, A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Characterization, and Cdna Sequencing of a Novel Hydroproline-Containing Factor Secreted by the Strawberry Pathogen Phytophtora Cactorum
Authors: Orsomando, G. / Lorenzi, M. / Raffaelli, M. / Dalla Rizza, N. / Mezzetti, M. / Ruggeri, S.
#2: Journal: Cell.Mol.Life.Sci. / Year: 2003
Title: Pcf Protein from Phytophthora Cactorum and its Recombinant Homologue Elicit Phenylalanine Ammonia Lyase Activation in Tomato
Authors: Orsomando, G. / Lorenzi, M. / Ferrari, E. / Dechiara, C. / Spisni, A. / Ruggieri, S.
History
DepositionJan 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Revision 1.2Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHYTOTOXIC PROTEIN PCF


Theoretical massNumber of molelcules
Total (without water)5,6171
Polymers5,6171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
Representative

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Components

#1: Protein PHYTOTOXIC PROTEIN PCF


Mass: 5617.179 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROLINE 49 IS HYDROXYLATED / Source: (gene. exp.) PHYTOPHTHORA CACTORUM (eukaryote) / Strain: P381 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: Q94FS7
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-NOESY
1212D-TOCSY
1312D-HSQC
1413D-TOCSY-HSQC
1513D-NOESY-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE ON 15N-LABELED PCF

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Sample preparation

DetailsContents: 90%WATER/10%D2O
Sample conditionsIonic strength: 10 mM / pH: 5 / Pressure: 1.0 atm / Temperature: 293.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DiscoverBRUNGERrefinement
Discoverstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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