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- PDB-7poo: Crystal structure of profragilysin-3 (proBFT-3) from Bacteroides ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7poo | ||||||
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Title | Crystal structure of profragilysin-3 (proBFT-3) from Bacteroides fragilis in complex with foliosidine in P212121. | ||||||
![]() | BFT-3 | ||||||
![]() | HYDROLASE / protease / zymogen / proteolysis / enterotoxin / fragilysin | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eckhard, U. / Guevara, T. / Gomis-Ruth, F.X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Repositioning small molecule drugs as allosteric inhibitors of the BFT-3 toxin from enterotoxigenic Bacteroides fragilis. Authors: Jimenez-Alesanco, A. / Eckhard, U. / Asencio Del Rio, M. / Vega, S. / Guevara, T. / Velazquez-Campoy, A. / Gomis-Ruth, F.X. / Abian, O. #1: ![]() Title: Structure, function and latency regulation of a bacterial enterotoxin potentially derived from a mammalian adamalysin/ADAM xenolog. Authors: Goulas, T. / Arolas, J.L. / Gomis-Ruth, F.X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.4 KB | Display | ![]() |
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PDB format | ![]() | 239.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pndC ![]() 7polC ![]() 7poqC ![]() 7pouC ![]() 3p24S C: citing same article ( S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45139.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ProBFT-3 (A18-D397) with a TEV-cleavable N-terminal His6-tag. Affinity tag was removed prior crystallization. Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 105 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/7WK.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/7WK.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PRO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.18 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 25 % (w/v) PEG 3350 0.2 M ammonium acetate 0.1M Bis Tris pH 5.5 Cryoprotection by soaking for 15-30 seconds in mother liquor supplemented with 2.5M L-proline. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→157.5 Å / Num. obs: 25344 / % possible obs: 98.1 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.184 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.7→2.73 Å / Rmerge(I) obs: 0.962 / Num. unique obs: 724 / CC1/2: 0.73 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3p24 Resolution: 2.7→73.47 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.861 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.914 / SU Rfree Blow DPI: 0.308 / SU Rfree Cruickshank DPI: 0.311
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Displacement parameters | Biso mean: 68.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→73.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.73 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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