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Open data
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Basic information
Entry | Database: PDB / ID: 7avm | ||||||
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Title | Crystal Structure of Pro-Rhodesain C150A | ||||||
![]() | Cysteine protease | ||||||
![]() | HYDROLASE / African trypanosomes / Sleeping Sickness / human african trypanosomiasis / cysteine protease / zymogen / pro-enzyme / rhodesain | ||||||
Function / homology | ![]() proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Johe, P. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Kersten, C. / Hellmich, U. | ||||||
![]() | ![]() Title: Structure, interdomain dynamics, and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes. Authors: Johe, P. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Kersten, C. / Hellmich, U.A. #1: ![]() Title: Structural basis of autoinhibition in the T. brucei rhodesiense cathepsin L zymogen pro-rhodesain and pH-dependent cleavage Authors: Johe, P. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Kersten, C. / Hellmich, U. #2: ![]() Title: Structural basis of autoinhibition in the T. brucei rhodesiense cathepsin L zymogen pro-rhodesain and pH-dependent cleavage Authors: Johe, P. / Kersten, C. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Hellmich, U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.1 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ex8S S: Starting model for refinement |
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Similar structure data |
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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: 35897.926 Da / Num. of mol.: 1 / Mutation: C150A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rhodesain / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.48 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 40 mM sodium citrate, 30% PEG-6000, Lead(II) acetate (saturated),cryoprotection with glycerol 10% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.92 Å / Num. obs: 7512 / % possible obs: 97.23 % / Redundancy: 20.6 % / Biso Wilson estimate: 41.24 Å2 / CC1/2: 0.919 / CC star: 0.979 / Net I/σ(I): 214.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 729 / CC1/2: 0.905 / CC star: 0.975 / % possible all: 92.73 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6EX8 Resolution: 2.8→37.92 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.3682 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: 47.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→37.92 Å
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Refine LS restraints |
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LS refinement shell |
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