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Yorodumi- PDB-6rfm: Bordetella pertussis adenylate cyclase toxin transmembrane segmen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rfm | ||||||
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Title | Bordetella pertussis adenylate cyclase toxin transmembrane segment 411-490 in DPC micelles | ||||||
Components | Bifunctional hemolysin/adenylate cyclase | ||||||
Keywords | TOXIN / adenylate cyclase / Bordetella pertussis / membrane protein / calcium binding | ||||||
Function / homology | Function and homology information calcium ion sequestering activity / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / ion binding / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration ...calcium ion sequestering activity / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / ion binding / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding / calcium ion binding / host cell plasma membrane / extracellular region / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Bordetella pertussis (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Masin, J. / Bumba, L. / Veverka, V. | ||||||
Citation | Journal: Biochim Biophys Acta Biomembr / Year: 2020 Title: Negative charge of the AC-to-Hly linking segment modulates calcium-dependent membrane activities of Bordetella adenylate cyclase toxin. Authors: Sukova, A. / Bumba, L. / Srb, P. / Veverka, V. / Stanek, O. / Holubova, J. / Chmelik, J. / Fiser, R. / Sebo, P. / Masin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rfm.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rfm.ent.gz | 933.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rfm_validation.pdf.gz | 559.4 KB | Display | wwPDB validaton report |
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Full document | 6rfm_full_validation.pdf.gz | 850.4 KB | Display | |
Data in XML | 6rfm_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 6rfm_validation.cif.gz | 111 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/6rfm ftp://data.pdbj.org/pub/pdb/validation_reports/rf/6rfm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8226.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: cya, cyaA, BN118_0468 / Production host: Escherichia coli (E. coli) References: UniProt: J7QLC0, UniProt: P0DKX7*PLUS, adenylate cyclase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: micelle Contents: 450 uM [U-13C; U-15N] Cya411-490, 25 mM sodium phosphate, 100 mM sodium chloride, 1 mM TCEP, 100 mM [U-2H] DPC, 90% H2O/10% D2O Label: s1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 125 mM / Label: c1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 50 |