[English] 日本語
Yorodumi- PDB-6wa1: Dimeric form of the trans-stabilized Hemolysin II C-terminal domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wa1 | ||||||
---|---|---|---|---|---|---|---|
Title | Dimeric form of the trans-stabilized Hemolysin II C-terminal domain | ||||||
Components | Hemolysin II | ||||||
Keywords | TOXIN / domain swapped dimer | ||||||
Function / homology | Bi-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 species | Bacillus cereus (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Kaplan, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6wa1.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wa1.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6wa1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/6wa1 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/6wa1 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data | |
Other databases |
|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | 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 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Type: 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 |
| ||||||||||||||||||||||||
Sample conditions | Ionic strength: 0 M / Label: 13C_15N_P87M / pH: 6.5 / Pressure: 1 atm / Temperature: 303.15 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 8 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 25 |