[English] 日本語
![](img/lk-miru.gif)
- PDB-3mfe: Crystal Structure of Mycobacterium Tuberculosis Proteasome open-g... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3mfe | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant with H0 movement | ||||||
![]() |
| ||||||
![]() | HYDROLASE / Catalytic Domain / Hydrogen Bonding / Mycobacterium tuberculosis / Oxazolidinones / Protease Inhibitors / Proteasome Endopeptidase Complex / Protein Carbonylation / Protein Conformation / Protein Subunits / Substrate Specificity / Thiazoles / helix movement | ||||||
Function / homology | ![]() symbiont-mediated perturbation of host defenses / zymogen binding / cell wall / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / cell wall / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / peptidoglycan-based cell wall / proteolysis involved in protein catabolic process / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, D. / Li, H. | ||||||
![]() | ![]() Title: Structural basis for the assembly and gate closure mechanisms of the Mycobacterium tuberculosis 20S proteasome. Authors: Li, D. / Li, H. / Wang, T. / Pan, H. / Lin, G. / Li, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 938 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 690.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 838.5 KB | Display | |
Data in XML | ![]() | 225.3 KB | Display | |
Data in CIF | ![]() | 296.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mi0C ![]() 3mkaC ![]() 3hfaS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25300.258 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O33245, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex #2: Protein | Mass: 25274.264 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O33245, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex #3: 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: O33244, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 13.5% PEG 6000, 60mM sodium citrate, pH 5.8, 0.1M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50 Å / Num. all: 203735 / Num. obs: 195691 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.1 / Num. unique all: 18667 / % possible all: 88.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3HFA Resolution: 2.6→29.87 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4680824.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.8279 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|