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- PDB-2lai: Hyaloperonospora arabidopsidis Effector Protein ATR13 -

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Basic information

Entry
Database: PDB / ID: 2lai
TitleHyaloperonospora arabidopsidis Effector Protein ATR13
ComponentsAvirulence protein ATR13
KeywordsSIGNALING PROTEIN / nucleolar localization
Function / homology
Function and homology information


host cell cytoplasm / extracellular region
Similarity search - Function
Avirulence protein ATR13 / Avirulence protein ATR13 / ATR13 superfamily / Avirulence protein ATR13, RxLR effector / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Avirulence protein ATR13
Similarity search - Component
Biological speciesHyaloperonospora parasitica (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsLeonelli, L. / Pelton, J.G. / Wemmer, D.E. / Staskawicz, B.J.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structural Elucidation and Functional Characterization of the Hyaloperonospora arabidopsidis Effector Protein ATR13.
Authors: Leonelli, L. / Pelton, J. / Schoeffler, A. / Dahlbeck, D. / Berger, J. / Wemmer, D.E. / Staskawicz, B.
History
DepositionMar 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Avirulence protein ATR13


Theoretical massNumber of molelcules
Total (without water)11,3061
Polymers11,3061
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Avirulence protein ATR13


Mass: 11305.883 Da / Num. of mol.: 1 / Fragment: sequence database residues 54-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyaloperonospora parasitica (eukaryote)
Gene: Atr13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5G7K8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: ATR13 Chemical Shifts and Structure
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CO
1623D 1H-15N NOESY
1713D (H)CCH-TOCSY
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D 1H-15N TOCSY
11113D H(CCO)NH
11213D C(CO)NH
11313D (H)CCH-COSY
11413D 1H-13C NOESY aliphatic
11523D HNHA
11632D 1H-13C HSQC
11742D IPAP
11822D 15N Heteronuclear NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] ATR13, 20 mM potassium phosphate, 150 mM sodium chloride, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 15N] ATR13, 20 mM potassium phosphate, 150 mM sodium chloride, 10 % [U-99% 2H] D2O/90% H2O90% H2O/10% D2O
31 mM [U-10% 13C; U-99% 15N] ATR13, 20 mM potassium phosphate, 150 mM sodium chloride, 10 % [U-99% 2H] D2O/90% H2O90% H2O/10% D2O
41 mM [U-98% 15N] ATR13, 20 mM potassium phosphate, 150 mM sodium chloride, 10 % [U-99% 2H] D2O, 12 mg/ml Pf1 phage, 90% H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMATR13-1[U-100% 13C; U-100% 15N]1
20 mMpotassium phosphate-21
150 mMsodium chloride-31
10 %D2O-4[U-99% 2H]1
1 mMATR13-5[U-98% 15N]2
20 mMpotassium phosphate-62
150 mMsodium chloride-72
10 %D2O-8[U-99% 2H]2
1 mMATR13-9[U-10% 13C; U-99% 15N]3
20 mMpotassium phosphate-103
150 mMsodium chloride-113
10 %D2O-12[U-99% 2H]3
1 mMATR13-13[U-98% 15N]4
20 mMpotassium phosphate-144
150 mMsodium chloride-154
10 %D2O-16[U-99% 2H]4
12 mg/mLPf1 phage-174
Sample conditionsIonic strength: 210 / pH: 7.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002
Bruker Avance IIBrukerAVANCE II9003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 448 / NOE intraresidue total count: 155 / NOE long range total count: 71 / NOE medium range total count: 80 / NOE sequential total count: 142
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.025 Å / Distance rms dev error: 0.004 Å

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