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Yorodumi- PDB-8b9o: Structure of the C-terminal domain of ClpC2 from Mycobacterium sm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b9o | |||||||||
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Title | Structure of the C-terminal domain of ClpC2 from Mycobacterium smegmatis | |||||||||
Components | Clp amino terminal domain protein | |||||||||
Keywords | CYTOSOLIC PROTEIN / stress resistance protein | |||||||||
Function / homology | Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / phospho-arginine / Clp amino terminal domain protein Function and homology information | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Meinhart, A. / Hoi, D.M. / Clausen, T. | |||||||||
Funding support | European Union, Austria, 2items
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Citation | Journal: Cell / Year: 2023 Title: Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival. Authors: Hoi, D.M. / Junker, S. / Junk, L. / Schwechel, K. / Fischel, K. / Podlesainski, D. / Hawkins, P.M.E. / van Geelen, L. / Kaschani, F. / Leodolter, J. / Morreale, F.E. / Kleine, S. / Guha, S. ...Authors: Hoi, D.M. / Junker, S. / Junk, L. / Schwechel, K. / Fischel, K. / Podlesainski, D. / Hawkins, P.M.E. / van Geelen, L. / Kaschani, F. / Leodolter, J. / Morreale, F.E. / Kleine, S. / Guha, S. / Rumpel, K. / Schmiedel, V.M. / Weinstabl, H. / Meinhart, A. / Payne, R.J. / Kaiser, M. / Hartl, M. / Boehmelt, G. / Kazmaier, U. / Kalscheuer, R. / Clausen, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b9o.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b9o.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 8b9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b9o_validation.pdf.gz | 712.5 KB | Display | wwPDB validaton report |
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Full document | 8b9o_full_validation.pdf.gz | 713 KB | Display | |
Data in XML | 8b9o_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 8b9o_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/8b9o ftp://data.pdbj.org/pub/pdb/validation_reports/b9/8b9o | HTTPS FTP |
-Related structure data
Related structure data | 8b9uC 3wdbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16818.041 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2792 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QW35 |
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#2: Chemical | ChemComp-RPI / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.02 M of each amino acid and 0.1 M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. obs: 8941 / % possible obs: 98.9 % / Redundancy: 4.3 % / CC1/2: 0.998 / Rrim(I) all: 0.55 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 3.9 % / Num. unique obs: 610 / CC1/2: 0.669 / Rrim(I) all: 0.981 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WDB Resolution: 2→32.2 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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