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- PDB-7rb4: Crystal structure of Peptono Toxin, a diphtheria toxin homolog, f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rb4 | ||||||
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Title | Crystal structure of Peptono Toxin, a diphtheria toxin homolog, from Seinonella peptonophila | ||||||
![]() | Diphtheria toxin, C domain | ||||||
![]() | TOXIN / diphtheria toxin / DT / homolog / Seinonella peptonophila | ||||||
Function / homology | Diphtheria toxin, translocation domain / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain / IODIDE ION / Diphtheria toxin, C domain![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugiman-Marangos, S.N. / Gill, S.K. / Melnyk, R.A. | ||||||
![]() | ![]() Title: Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold. Authors: Sugiman-Marangos, S.N. / Gill, S.K. / Mansfield, M.J. / Orrell, K.E. / Doxey, A.C. / Melnyk, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.5 KB | Display | ![]() |
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PDB format | ![]() | 201.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ri3C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 67445.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-IOD / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1 uL SPT (15.8 mg/mL in 20 mM Tris pH 8.0, 150 mM NaCl) and 1 uL mother liquor (100 mM potassium iodide, 22% PEG3350) dehydrated over 200 uL of mother liquor |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 6, 2019 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 2.185→59.291 Å / Num. obs: 28929 / % possible obs: 92.7 % / Redundancy: 11.5 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.185→2.192 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.587 / Num. unique obs: 168 / CC1/2: 0.663 / Rpim(I) all: 0.353 / Rrim(I) all: 0.69 / % possible all: 54 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→59.29 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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