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- PDB-2mlw: New Cyt-like delta-endotoxins from Dickeya dadantii - CytC protein -

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Basic information

Entry
Database: PDB / ID: 2mlw
TitleNew Cyt-like delta-endotoxins from Dickeya dadantii - CytC protein
ComponentsType-1Ba cytolytic delta-endotoxin
KeywordsTOXIN / cytolysin fold / modified Greek key topology
Function / homologyDelta-endotoxin CytB / Delta-endotoxin CytB-like superfamily / Bacillus thuringiensis toxin / : / extracellular region / Type-1Ba cytolytic delta-endotoxin
Function and homology information
Biological speciesDickeya dadantii (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLoth, K. / Costechareyre, D. / Effantin, G. / Rahbe, Y. / Condemine, G. / Landon, C. / Da Silva, P.
CitationJournal: Sci Rep / Year: 2015
Title: New Cyt-like delta-endotoxins from Dickeya dadantii: structure and aphicidal activity.
Authors: Loth, K. / Costechareyre, D. / Effantin, G. / Rahbe, Y. / Condemine, G. / Landon, C. / da Silva, P.
History
DepositionMar 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type-1Ba cytolytic delta-endotoxin


Theoretical massNumber of molelcules
Total (without water)22,4121
Polymers22,4121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Type-1Ba cytolytic delta-endotoxin / CytC protein


Mass: 22412.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Gene: Dda3937_01343 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): NM522 / References: UniProt: E0SJ33

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D C(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11012D 1H-15N HSQC
11112D 1H-13C HSQC
11213D HN(CO)CA

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Sample preparation

DetailsContents: 0.3 mM [U-13C; U-15N] CytC, 50 mM Tris, 100 mM sodium chloride, 1 mM EDTA, 5 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMCytC-1[U-13C; U-15N]1
50 mMTris-21
100 mMsodium chloride-31
1 mMEDTA-41
5 mMDTT-51
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: ambient / Temperature: 298 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
NameVersionDeveloperClassification
VnmrJVariancollection
CcpNMR2.1.5CCPNdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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