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- PDB-6wa1: Dimeric form of the trans-stabilized Hemolysin II C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6wa1
TitleDimeric form of the trans-stabilized Hemolysin II C-terminal domain
ComponentsHemolysin II
KeywordsTOXIN / domain swapped dimer
Function / homologyBi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / cytolysis in another organism / extracellular region / Hemolysin II
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKaplan, A.R. / Alexandrescu, A.T.
Citation
Journal: Protein Sci. / Year: 2021
Title: Protein yoga: Conformational versatility of the Hemolysin II C-terminal domain detailed by NMR structures for multiple states.
Authors: Kaplan, A.R. / Olson, R. / Alexandrescu, A.T.
#1: Journal: Sci Rep / Year: 2017
Title: NMR structure of the Bacillus cereus hemolysin II C-terminal domain reveals a novel fold.
Authors: Kaplan, A.R. / Kaus, K. / De, S. / Olson, R. / Alexandrescu, A.T.
#2: Journal: Biomol.Nmr Assign. / Year: 2014
Title: NMR assignments for the cis and trans forms of the hemolysin II C-terminal domain.
Authors: Kaplan, A.R. / Maciejewski, M.W. / Olson, R. / Alexandrescu, A.T.
History
DepositionMar 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
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 1.4May 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: Hemolysin II
B: Hemolysin II


Theoretical massNumber of molelcules
Total (without water)20,9232
Polymers20,9232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: based on information from NMR using DOSY experiments, and T2 relaxation rates.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1920 Å2
ΔGint-15 kcal/mol
Surface area11330 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Hemolysin II


Mass: 10461.706 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 319-412) / Mutation: P87M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_3523 / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q81AN8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D 1H-15N NOESY
151isotropic13D 1H-15N TOCSY
161isotropic13D 1H-13C NOESY (edited)
171isotropic13D 1H-13C NOESY (filtered)

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-99% 13C; U-99% 15N] HlyIIC, 20 mM sodium phosphate, 1 mM EDTA, 0.05 % w/v sodium azide, 1 mM AEBSF protease inhibitor, 90% H2O/10% D2O
Label: 13C_15N_P87M / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMHlyIIC[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenone1
1 mMEDTAnone1
0.05 % w/vsodium azidenone1
1 mMAEBSF protease inhibitornone1
Sample conditionsIonic strength: 0 M / Label: 13C_15N_P87M / pH: 6.5 / Pressure: 1 atm / Temperature: 303.15 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
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNdata analysis
TALOSTALOS-NCornilescu, Delaglio and Baxgeometry optimization
CcpNmr Analysis2.4CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 25

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