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- PDB-2n67: C-terminal domain of Hemolysin II-P87M-BMRB -

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Basic information

Entry
Database: PDB / ID: 2n67
TitleC-terminal domain of Hemolysin II-P87M-BMRB
ComponentsHemolysin II
KeywordsTOXIN / hemolysin / novel fold / pore-forming toxin / conformational heterogeneity
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 / molecular dynamics
Model detailsclosest to the average, model1
AuthorsKaplan, A.R. / Maciejewski, M.W. / Olson, R. / Alexandrescu, A.T.
Citation
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.
#1: 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
DepositionAug 13, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.3May 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
B: Hemolysin II


Theoretical massNumber of molelcules
Total (without water)10,4621
Polymers10,4621
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)25 / 250structures 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.: 1 / Fragment: C-terminal domain (UNP residues 319-412) / Mutation: P87M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC_3523 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q81AN8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D HNCO
1313D HN(CA)CO
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1612D 1H-1H TOCSY
1722D DQF-COSY
1822D 1H-1H NOESY
1913D CCH-TOCSY
11033D HNHA
11133D HNHB
11233D 1H-15N TOCSY
11313D 1H-13C NOESY aliphatic
11433D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-99% 13C; U-99% 15N] p87m-HlyIIC, 20 mM sodium phosphate, 1 mM EDTA, 1 mM AEBSF, 0.05% w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-99% 15N] p87m-HlyIIC, 20 mM sodium phosphate, 1 mM EDTA, 1 mM AEBSF, 0.05% w/v sodium azide, 100% D2O100% D2O
30.4 mM [U-99% 15N] p87m-HlyIIC, 20 mM sodium phosphate, 1 mM EDTA, 1 mM AEBSF, 0.05% w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMp87m-HlyIIC-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
1 mMEDTA-31
1 mMAEBSF-41
0.05 w/vsodium azide-51
0.4 mMp87m-HlyIIC-6[U-99% 15N]2
20 mMsodium phosphate-72
1 mMEDTA-82
1 mMAEBSF-92
0.05 w/vsodium azide-102
0.4 mMp87m-HlyIIC-11[U-99% 15N]3
20 mMsodium phosphate-123
1 mMEDTA-133
1 mMAEBSF-143
0.05 w/vsodium azide-153
Sample conditionspH: 6 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
ANALYSIS2.1CCPNchemical shift assignment
ANALYSIS2.1CCPNdata analysis
FELIX-NMRAccelrys Software Inc.processing
FELIX-NMRAccelrys Software Inc.structure solution
FELIX-NMRSchwieters, Kuszewski, Tjandra and Cloreprocessing
FELIX-NMRSchwieters, Kuszewski, Tjandra and Clorestructure solution
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
TALOSTALOS-NCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1538 / NOE intraresidue total count: 690 / NOE long range total count: 271 / NOE medium range total count: 160 / NOE sequential total count: 417 / Protein chi angle constraints total count: 38 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 80 / Protein psi angle constraints total count: 80
NMR representativeSelection criteria: closest to the average
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 250 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0.04 Å / Distance rms dev error: 0.002 Å

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