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- PDB-6d53: Trans form of HemolysinII c-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6d53
TitleTrans form of HemolysinII c-terminal domain
ComponentsHemolysin II
KeywordsTOXIN / pore-forming toxin / proline isomerization / 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
AuthorsKaplan, A.R. / Alexandrescu, A.T. / Olson, R.
CitationJournal: To Be Published
Title: Trans form of HemolysinII c-terminal domain
Authors: Kaplan, A.R. / Alexandrescu, A.T. / Olson, R.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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
C: Hemolysin II


Theoretical massNumber of molelcules
Total (without water)10,8411
Polymers10,8411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, also evident from NMR experiments.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5350 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: 10841.098 Da / Num. of mol.: 1 / Fragment: C-terminal Domain, residues 319-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (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-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / 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
111isotropic13D HN(CA)CB
121isotropic13D HN(CO)CA
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic12D 1H-15N HSQC
162isotropic23D HNHA
172isotropic23D HNHB
183isotropic22D DQF-COSY
193isotropic22D 1H-1H NOESY
1101isotropic12D 1H-13C HSQC
1111isotropic12D 1H-1H TOCSY
1121isotropic13D (H)CCH-TOCSY
1131isotropic13D CCH-TOCSY
1142isotropic23D 1H-15N TOCSY
1151isotropic13D 1H-13C NOESY aliphatic
1162isotropic23D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 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% D2O13C15N_sample90% H2O/10% D2O
solution21.0 mM [U-99% 15N] HlyIIC, 20 mM sodium phosphate, 1 mM EDTA, 1 mM AEBSF protease inhibitor, 0.05 % w/v sodium azide, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution31.0 mM [U-99% 15N] HlyIIC, 20 mM sodium phosphate, 1.0 mM EDTA, 1.0 mM AEBSF protease inhibitor, 0.05 % w/v sodium azide, 100% D2OD2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMHlyIIC[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenone1
1 mMEDTAnone1
0.05 % w/vsodium azidenone1
1 mMAEBSF protease inhibitornone1
1.0 mMHlyIIC[U-99% 15N]2
20 mMsodium phosphatenone2
1 mMEDTAnone2
1 mMAEBSF protease inhibitornone2
0.05 % w/vsodium azidenone2
1.0 mMHlyIIC[U-99% 15N]3
20 mMsodium phosphatenone3
1.0 mMEDTAnone3
1.0 mMAEBSF protease inhibitornone3
0.05 % w/vsodium azidenone3
Sample conditionsIonic strength: 0 M / Label: 1 / pH: 6 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA8001cryoprobe
Varian INOVAVarianINOVA6002cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNMR2.4CCPNchemical shift assignment
FelixAccelrys Software Inc.processing
CcpNMR2.4CCPNdata analysis
CcpNMRCCPNpeak picking
TALOS-NCornilescu, Delaglio and Baxgeometry optimization
XPLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
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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