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- PDB-2lf6: Solution NMR structure of HopABPph1448_220_320 from Pseudomonas s... -

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Basic information

Entry
Database: PDB / ID: 2lf6
TitleSolution NMR structure of HopABPph1448_220_320 from Pseudomonas syringae pv. phaseolicola str. 1448A, Midwest Center for Structural Genomics target APC40132.4 and Northeast Structural Genomics Consortium target PsT3A
ComponentsEffector protein hopAB1
KeywordsSIGNALING PROTEIN / type III effector / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Midwest Center for Structural Genomics / MCSG / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


: / extracellular region
Similarity search - Function
Effector protein HopAB, BAK1-interacting domain / Effector protein HopAB, E3 ubiquitin ligase domain / Effector protein HopAB, E3 ubiquitin ligase domain superfamily / AvrPtoB E3 ubiquitin ligase / Effector protein HopAB, BAK1-binding domain / Effector protein HopAB, BAK1-binding domain superfamily / Avirulence AvrPtoB, BAK1-binding domain / Effector protein HopAB, Pto-binding domain / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Effector protein hopAB1
Similarity search - Component
Biological speciesPseudomonas syringae pv. phaseolicola 1448A (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, B. / Yee, A. / Houliston, S. / Semesi, A. / Garcia, M. / Singer, A.U. / Savchenko, A. / Montelione, G.T. / Joachimiak, A. / Arrowsmith, C.H. ...Wu, B. / Yee, A. / Houliston, S. / Semesi, A. / Garcia, M. / Singer, A.U. / Savchenko, A. / Montelione, G.T. / Joachimiak, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Midwest Center for Structural Genomics (MCSG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: Biochemistry / Year: 2012
Title: Structural Analysis of HopPmaL Reveals the Presence of a Second Adaptor Domain Common to the HopAB Family of Pseudomonas syringae Type III Effectors.
Authors: Singer, A.U. / Wu, B. / Yee, A. / Houliston, S. / Xu, X. / Cui, H. / Skarina, T. / Garcia, M. / Semesi, A. / Arrowsmith, C.H. / Savchenko, A.
History
DepositionJun 28, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Feb 22, 2012Group: Structure summary
Revision 1.4Jun 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
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Effector protein hopAB1


Theoretical massNumber of molelcules
Total (without water)11,2761
Polymers11,2761
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Effector protein hopAB1


Mass: 11275.709 Da / Num. of mol.: 1 / Fragment: sequence database residues 220-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. phaseolicola 1448A (bacteria)
Strain: 1448A / Race 6 / Gene: hopAB1, virPphA, PSPPH_A0127 / Production host: Escherichia coli (E. coli) / References: UniProt: Q48B61

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HBHA(CO)NH
1413D HNCA
1513D (H)CCH-TOCSY
1613D CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C NOESY aromatic
11022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] HopAB1Pph1448_220_320, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
20.2 mM [U-7% 13C; U-100% 15N] HopAB1Pph1448_220_320, 10 mM [U-100% 2H] TRIS, 300 mM sodium chloride, 10 uM zinc sulphate, 10 mM [U-100% 2H] DTT, 0.01 % NaN3, 10 mM benzamidine, 1 x inhibitor cocktail, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHopAB1Pph1448_220_320-1[U-100% 13C; U-100% 15N]1
10 mMTRIS-2[U-100% 2H]1
300 mMsodium chloride-31
10 uMzinc sulphate-41
10 mMDTT-5[U-100% 2H]1
0.01 %NaN3-61
10 mMbenzamidine-71
1 %inhibitor cocktail-81
0.2 mMHopAB1Pph1448_220_320-9[U-7% 13C; U-100% 15N]2
10 mMTRIS-10[U-100% 2H]2
300 mMsodium chloride-112
10 uMzinc sulphate-122
10 mMDTT-13[U-100% 2H]2
0.01 %NaN3-142
10 mMbenzamidine-152
1 %inhibitor cocktail-162
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MDDGUI1Gutmanas, Arrowsmithprocessing
Sparky3.95Goddarddata analysis
FMCGUI2.4Lemak, Arrowsmithchemical shift assignment
FMCGUI2.4Lemak, Arrowsmithdata analysis
FAWN1Lemak, Arrowsmithchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionenmr structure quality assessment
PSVSBhattacharya and Montelionenmr structure quality assessment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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