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- PDB-2kq5: Solution NMR structure of a section of the repeat domain of the t... -

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Basic information

Entry
Database: PDB / ID: 2kq5
TitleSolution NMR structure of a section of the repeat domain of the type III effector protein PthA
ComponentsAvirulence protein
KeywordsUNKNOWN FUNCTION / Ptha / 1.5 repeat units
Function / homologyHelix Hairpins - #500 / TAL effector repeat / TAL effector repeat / Helix Hairpins / Helix non-globular / Special / Avirulence protein
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsNeves, J.L. / Sforca, M.L. / Murakami, M.T. / Benedetti, C.E. / Zeri, A.C.
CitationJournal: To be Published
Title: An NMR-based structural model of the PthA repeat region reveals a TPR fold that would account for protein-protein and protein-DNA interactions
Authors: Neves, J.L. / Sforca, M.L. / Murakami, M.T. / Benedetti, C.E. / Zeri, A.C.
History
DepositionOct 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Avirulence protein


Theoretical massNumber of molelcules
Total (without water)5,2941
Polymers5,2941
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)21 / 100structures with the lowest energy
RepresentativeModel #16lowest energy

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Components

#1: Protein Avirulence protein


Mass: 5294.024 Da / Num. of mol.: 1 / Fragment: UNP residues 629-679 / Source method: obtained synthetically
Source: (synth.) Xanthomonas axonopodis pv. citri (bacteria)
References: UniProt: Q8PRN6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: 1.5 repeat peptide of the PthA protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H COSY
1312D 1H-1H NOESY
NMR detailsText: collection

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Sample preparation

DetailsContents: 1.0 mM protein, 20 mM sodium phosphate, 70 mM SDS, 1 mM DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.0 mMentity-11
20 mMsodium phosphate-21
7 mMSDS-31
1 mMDTT-41
Sample conditionspH: 5 / Pressure: ambient / Temperature: 293 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
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry / 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: 21

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