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Yorodumi- PDB-5iet: Crystal Structure of Mycobacterium Tuberculosis ATP-independent P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iet | ||||||
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Title | Crystal Structure of Mycobacterium Tuberculosis ATP-independent Proteasome activator | ||||||
Components | Bacterial proteasome activator | ||||||
Keywords | GENE REGULATION / Activator / Apoptosis | ||||||
Function / homology | Function and homology information proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome binding / peptidoglycan-based cell wall / protein homooligomerization / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.88 Å | ||||||
Authors | Bai, L. / Hu, K. / Wang, T. / Jastrab, J.B. / Darwin, K.H. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. Authors: Bai, L. / Hu, K. / Wang, T. / Jastrab, J.B. / Darwin, K.H. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iet.cif.gz | 57.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iet.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 5iet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iet_validation.pdf.gz | 461.7 KB | Display | wwPDB validaton report |
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Full document | 5iet_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 5iet_validation.xml.gz | 11 KB | Display | |
Data in CIF | 5iet_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/5iet ftp://data.pdbj.org/pub/pdb/validation_reports/ie/5iet | HTTPS FTP |
-Related 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: 17133.516 Da / Num. of mol.: 2 / Fragment: residues 19-157 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: AFL40_3934 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K2KYP6, UniProt: P9WKX3*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MPD / ( #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: 4.89 Å3/Da / Density % sol: 74.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.2 M ammonium acetate, 0.1 M sodium citrate 29% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→42 Å / Num. obs: 16296 / % possible obs: 99.9 % / Redundancy: 19.3 % / Net I/σ(I): 15.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.88→41.99 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.806 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.219 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.634 Å2
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Refinement step | Cycle: 1 / Resolution: 2.88→41.99 Å
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Refine LS restraints |
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