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Yorodumi- PDB-6ocw: Crystal Structure of Mycobacterium tuberculosis Proteasome in Com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ocw | ||||||
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Title | Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with Phenylimidazole-based Inhibitor A85 | ||||||
Components | (Proteasome subunit ...) x 2 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Mycobacterium tuberculosis / proteasome inhibitor / phenylimidazole / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host defenses / zymogen binding / 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 ...symbiont-mediated perturbation of host defenses / zymogen binding / 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Hsu, H.C. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: Selective Phenylimidazole-Based Inhibitors of theMycobacterium tuberculosisProteasome. Authors: Zhan, W. / Hsu, H.C. / Morgan, T. / Ouellette, T. / Burns-Huang, K. / Hara, R. / Wright, A.G. / Imaeda, T. / Okamoto, R. / Sato, K. / Michino, M. / Ramjee, M. / Aso, K. / Meinke, P.T. / ...Authors: Zhan, W. / Hsu, H.C. / Morgan, T. / Ouellette, T. / Burns-Huang, K. / Hara, R. / Wright, A.G. / Imaeda, T. / Okamoto, R. / Sato, K. / Michino, M. / Ramjee, M. / Aso, K. / Meinke, P.T. / Foley, M. / Nathan, C.F. / Li, H. / Lin, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ocw.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ocw.ent.gz | 965.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ocw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ocw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ocw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ocw_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 6ocw_validation.cif.gz | 73 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/6ocw ftp://data.pdbj.org/pub/pdb/validation_reports/oc/6ocw | HTTPS FTP |
-Related structure data
Related structure data | 6oczC 6odeC 5ts0S 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
-Proteasome subunit ... , 2 types, 28 molecules ABCDEFGOPQRSTUHIJKLMNVWXYZab
#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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: prcA, Rv2109c / Production host: Escherichia coli (E. coli) References: UniProt: P9WHU1, proteasome endopeptidase complex #2: Protein | Mass: 24445.383 Da / Num. of mol.: 14 / Fragment: UNP residues 58-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: prcB, Rv2110c / Production host: Escherichia coli (E. coli) References: UniProt: P9WHT9, proteasome endopeptidase complex |
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-Non-polymers , 4 types, 980 molecules
#3: Chemical | ChemComp-DMF / #4: Chemical | ChemComp-M6M / #5: Chemical | ChemComp-CIT / #6: 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: 2.73 Å3/Da / Density % sol: 55.02 % |
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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, 14% PEG3350, 35% dimethyl formamide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 15, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→198.65 Å / Num. obs: 224759 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 33844 / CC1/2: 0.734 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5TS0 Resolution: 2.6→42.82 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 32.22 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→42.82 Å
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