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- PDB-7e3e: Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e3e | |||||||||
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Title | Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant | |||||||||
![]() | Cysteine peptidase C (CPC) | |||||||||
![]() | HYDROLASE / In cell crystal | |||||||||
Function / homology | ![]() post-transcriptional regulation of gene expression / proteolysis involved in protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Abe, S. / Pham, T.T. / Negishi, H. / Yamashita, K. / Hirata, K. / Ueno, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Authors: Abe, S. / Pham, T.T. / Negishi, H. / Yamashita, K. / Hirata, K. / Ueno, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.2 KB | Display | ![]() |
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PDB format | ![]() | 56.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7e3fC ![]() 7e3gC ![]() 4hwyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37207.676 Da / Num. of mol.: 1 / Mutation: R91C, T223C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 927/4 GUTat10.1 / Gene: Tb927.6.560 / Production host: ![]() ![]() References: UniProt: D6XHE1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.48 % |
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Crystal grow | Temperature: 293 K / Method: in cell / Details: In cell crystallization |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 20010 / % possible obs: 100 % / Redundancy: 558 % / CC1/2: 0.99 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.3→2.32 Å / Num. unique obs: 496 / CC1/2: 0.374 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4hwy Resolution: 2.3→46.764 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.498 / SU ML: 0.189 / Cross valid method: FREE R-VALUE / ESU R: 0.275 / ESU R Free: 0.233
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.816 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→46.764 Å
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Refine LS restraints |
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LS refinement shell |
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