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Yorodumi- PDB-3h6f: Crystal Structure of Mycobacterium Tuberculosis Proteasome Modifi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h6f | ||||||
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Title | Crystal Structure of Mycobacterium Tuberculosis Proteasome Modified by inhibitor HT1171 | ||||||
Components |
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Keywords | HYDROLASE / Binding Sites / Oxazolidin-2-one / Mycobacterium tuberculosis / Protease Inhibitors / Proteasome Endopeptidase Complex / Protein Subunits / Substrate Specificity / Proteasome | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host defenses / zymogen binding / cell wall / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / proteasomal protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / cell wall / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / proteasomal protein catabolic process / modification-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Li, D. / Li, H. / Lin, G. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Inhibitors selective for mycobacterial versus human proteasomes. Authors: Lin, G. / Li, D. / de Carvalho, L.P. / Deng, H. / Tao, H. / Vogt, G. / Wu, K. / Schneider, J. / Chidawanyika, T. / Warren, J.D. / Li, H. / Nathan, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h6f.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3h6f.ent.gz | 955.6 KB | Display | PDB format |
PDBx/mmJSON format | 3h6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/3h6f ftp://data.pdbj.org/pub/pdb/validation_reports/h6/3h6f | HTTPS FTP |
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-Related structure data
Related structure data | 3h6iC 3hf9C 3hfaC 2fhgS 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: 26911.039 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcA, Rv2109c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O33244, UniProt: P9WHU1*PLUS, proteasome endopeptidase complex #2: Protein | Mass: 25300.258 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2170, prcB, Rv2110c / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O33245, UniProt: P9WHT9*PLUS, proteasome endopeptidase complex #3: Chemical | ChemComp-DMF / #4: Water | ChemComp-HOH / | Nonpolymer details | THE HETGROUP OZT IN THE STRUCTURE IS REFERRED TO AS OXZ IN A RELEVANT PUBLICATIO | |
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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: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 12% PEG 6000, 60 mM sodium citrate, pH 5.8, 0.1M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2008 |
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: 2.51→34 Å / Num. all: 247496 / Num. obs: 235346 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.4 / Num. unique all: 20632 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FHG Resolution: 2.51→29.83 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 110048.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME. BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 6.67316 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.51→29.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
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Xplor file |
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