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- PDB-5jhj: M. Oryzae effector AVR-Pia mutant H3 -

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Basic information

Entry
Database: PDB / ID: 5jhj
TitleM. Oryzae effector AVR-Pia mutant H3
ComponentsAntivirulence protein AVR-Pia
KeywordsUNKNOWN FUNCTION / Avirulence effector Magnaporthe Oryzae / Structure from MOLMOL / RGA5-BINDING PROTEIN
Function / homologyAntivirulence protein AVR-Pia
Function and homology information
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodSOLUTION NMR / simulated annealing
AuthorsPadilla, A. / deGuillen, K.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR- 10-INSB-05-0 France
CitationJournal: Plant Cell / Year: 2017
Title: Recognition of the Magnaporthe oryzae Effector AVR-Pia by the Decoy Domain of the Rice NLR Immune Receptor RGA5.
Authors: Ortiz, D. / de Guillen, K. / Cesari, S. / Chalvon, V. / Gracy, J. / Padilla, A. / Kroj, T.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2018Group: Data collection / Experimental preparation
Category: pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details
Item: _pdbx_nmr_exptl.conditions_id
Revision 1.4May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.5Oct 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 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antivirulence protein AVR-Pia


Theoretical massNumber of molelcules
Total (without water)10,8301
Polymers10,8301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6060 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Antivirulence protein AVR-Pia


Mass: 10830.049 Da / Num. of mol.: 1 / Mutation: F24S, T46N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pia / Variant: H3 allele / Plasmid: PET-SP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9RX08
Has protein modificationY

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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
121isotropic13D 1H-15N NOESY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-1H TOCSY
152isotropic22D 1H-13C HSQC
162isotropic22D 1H-13C TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-15N] AVR-Pia-H315N_sample90% H2O/10% D2O
solution21 mM [U-15N] AVR-Pia-H315N_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAVR-Pia-H3[U-15N]1
1 mMAVR-Pia-H3[U-15N]2
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 5.4 / Pressure: 1 bar / Temperature: 305 K

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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
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3.2Bruker Biospinchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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