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Yorodumi- PDB-5kwa: complete structure of the Mycobacterium tuberculosis proteasomal ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kwa | ||||||||||||
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Title | complete structure of the Mycobacterium tuberculosis proteasomal ATPase Mpa | ||||||||||||
Components | Proteasome-associated ATPase | ||||||||||||
Keywords | HYDROLASE / Proteasomal ATPase | ||||||||||||
Function / homology | Function and homology information ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / protein unfolding / cellular response to nitric oxide / proteasome complex ...ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / protein unfolding / cellular response to nitric oxide / proteasome complex / proteasomal protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||||||||
Authors | Wang, T. / WU, Y.J. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Mol. Microbiol. / Year: 2017 Title: Mycobacterium tuberculosis proteasomal ATPase Mpa has a beta-grasp domain that hinders docking with the proteasome core protease Authors: Wu, Y. / Hu, K. / Li, D. / Bai, L. / Yang, S. / Jastrab, J.B. / Xiao, S. / Hu, Y. / Zhang, S. / Darwin, K.H. / Wang, T. / Li, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kwa.cif.gz | 190 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kwa.ent.gz | 149.5 KB | Display | PDB format |
PDBx/mmJSON format | 5kwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/5kwa ftp://data.pdbj.org/pub/pdb/validation_reports/kw/5kwa | HTTPS FTP |
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-Related structure data
Related structure data | 5kzfC 3m9bS 3whkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54983.051 Da / Num. of mol.: 2 / Fragment: UNP residues 22-529 Source method: isolated from a genetically manipulated source Details: complete proteasomal ATPase binds with ATPrS / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mpa, ERS007663_01871 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T9XQP1, UniProt: P9WQN5*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.85 % / Description: hexagonal plate |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 100mM Tris-HCl, 20%PEG400, 200mM MgCl2, 5mM ATPrS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2013 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→43.45 Å / Num. obs: 32237 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 56.52 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.112 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.703 / CC1/2: 0.506 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M9B, 3WHK Resolution: 2.9→43.45 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.889 / SU B: 20.441 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R: 1.285 / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.887 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→43.45 Å
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Refine LS restraints |
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