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- PDB-2myv: Solution structure of M. oryzae protein AVR1-CO39 -

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Basic information

Entry
Database: PDB / ID: 2myv
TitleSolution structure of M. oryzae protein AVR1-CO39
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION
Function / homologyUncharacterized protein
Function and homology information
Biological speciesMagnaporthe grisea (fungus)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
Authorsde Guillen, K. / Kroj, T.
CitationJournal: Plos Pathog. / Year: 2015
Title: Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi.
Authors: de Guillen, K. / Ortiz-Vallejo, D. / Gracy, J. / Fournier, E. / Kroj, T. / Padilla, A.
History
DepositionJan 30, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,2431
Polymers11,2431
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 11243.166 Da / Num. of mol.: 1 / Fragment: residues 22-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q8J180

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1413D HNCO
1513D HNCA
1613D HN(COCA)CB
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1942D 1H-1H NOESY
11032D 1H-1H NOESY
11142D 1H-1H TOCSY
11242D DQF-COSY
11313D HN(CA)CB
11413D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] AVR1-CO39, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-15N] AVR1-CO39, 90% H2O/10% D2O90% H2O/10% D2O
31 mM AVR1-CO39, 100% D2O100% D2O
41 mM AVR1-CO39, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMAVR1-CO39-1[U-13C; U-15N]1
1 mMAVR1-CO39-2[U-15N]2
1 mMAVR1-CO39-33
1 mMAVR1-CO39-44
Sample conditionsIonic strength: 0.15 / pH: 6.8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CCPNCCPNdata analysis
CCPNCCPNpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+1.2Cornilescu, Delaglio and Baxdata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1286 / NOE long range total count: 384 / NOE medium range total count: 157 / Hydrogen bond constraints total count: 30
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 4 ° / Maximum upper distance constraint violation: 0.3 Å

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