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- PDB-2mm2: Solution Structures of Active Ptr ToxB and its inactive Homolog h... -

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Basic information

Entry
Database: PDB / ID: 2mm2
TitleSolution Structures of Active Ptr ToxB and its inactive Homolog highlight Protein Dynamics as a Modulator of Toxin activity.
ComponentsToxb
KeywordsPLANT PROTEIN
Function / homologyComplement Module; domain 1 - #110 / ToxB-like N-terminal, ascomycota / ToxB N-terminal domain / Complement Module; domain 1 / Ribbon / Mainly Beta / Toxb
Function and homology information
Biological speciesPyrenophora tritici-repentis (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBarbar, E. / Nyarko, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Solution NMR Structures of Pyrenophora tritici-repentis ToxB and Its Inactive Homolog Reveal Potential Determinants of Toxin Activity.
Authors: Nyarko, A. / Singarapu, K.K. / Figueroa, M. / Manning, V.A. / Pandelova, I. / Wolpert, T.J. / Ciuffetti, L.M. / Barbar, E.
History
DepositionMar 6, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Nov 27, 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
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxb


Theoretical massNumber of molelcules
Total (without water)6,6231
Polymers6,6231
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 Toxb


Mass: 6623.496 Da / Num. of mol.: 1 / Fragment: UNP residues 24-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrenophora tritici-repentis (fungus) / Gene: toxb / Production host: Pichia pastoris (fungus) / References: UniProt: Q8J0U6
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1713D (H)CCH-TOCSY
1813D HNCO
1913D HN(CA)CB
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 10 % D2O, 10 mM sodium phosphate, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 %D2O-11
10 mMsodium phosphate-21
Sample conditionsIonic strength: 10 / pH: 6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1076 / NOE intraresidue total count: 303 / NOE long range total count: 368 / NOE medium range total count: 132 / NOE sequential total count: 273 / Protein phi angle constraints total count: 46 / Protein psi angle constraints total count: 46
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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