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- PDB-5trr: Structure of Mycobacterium tuberculosis proteasome in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5trr | ||||||
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Title | Structure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide PKS2169 | ||||||
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![]() | HYDROLASE/HYDROLASE inhibitor / N / C-capped dipeptides / ![]() | ||||||
Function / homology | ![]() symbiont-mediated perturbation of host defenses / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsu, H.-C. / Fan, H. / Singh, P.K. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for the Species-Selective Binding of N,C-Capped Dipeptides to the Mycobacterium tuberculosis Proteasome. Authors: Hsu, H.C. / Singh, P.K. / Fan, H. / Wang, R. / Sukenick, G. / Nathan, C. / Lin, G. / Li, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 936.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5thoC ![]() 5trgC ![]() 5trsC ![]() 5tryC ![]() 5ts0C ![]() 3hfaS C: citing same article ( 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: 25971.975 Da / Num. of mol.: 14 / Fragment: UNP residues 10-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A5U4D5, UniProt: P9WHU1*PLUS, ![]() #2: Protein | ![]() Mass: 25274.264 Da / Num. of mol.: 14 / Fragment: UNP residues 58-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A5U4D6, UniProt: P9WHT9*PLUS, ![]() #3: Chemical | ChemComp-7HY / #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 60 mM sodium citrate (pH 6.2) and 14% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.1→47.2473073393 Å / Num. obs: 131508 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 73.5256458866 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.775 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3HFA Resolution: 3.103→47.247 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.103→47.247 Å
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Refine LS restraints |
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LS refinement shell |
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