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Yorodumi- PDB-6h23: Crystal structure of the hClpP Y118A mutant with an activating sm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h23 | |||||||||||||||
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Title | Crystal structure of the hClpP Y118A mutant with an activating small molecule | |||||||||||||||
Components | ATP-dependent Clp protease proteolytic subunit, mitochondrial | |||||||||||||||
Keywords | HYDROLASE / protease / small molecule / 14mer / serine protease / oligomerization | |||||||||||||||
Function / homology | Function and homology information membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix ...membrane protein proteolysis / endopeptidase Clp complex / endopeptidase Clp / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / ATPase binding / endopeptidase activity / mitochondrial matrix / serine-type endopeptidase activity / mitochondrion / proteolysis / identical protein binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.089 Å | |||||||||||||||
Authors | Kick, L.M. / Sieber, S.A. / Schneider, S. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Selective Activation of Human Caseinolytic Protease P (ClpP). Authors: Stahl, M. / Korotkov, V.S. / Balogh, D. / Kick, L.M. / Gersch, M. / Pahl, A. / Kielkowski, P. / Richter, K. / Schneider, S. / Sieber, S.A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h23.cif.gz | 462.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h23.ent.gz | 390.2 KB | Display | PDB format |
PDBx/mmJSON format | 6h23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/6h23 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/6h23 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25139.965 Da / Num. of mol.: 14 / Mutation: Y118A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLPP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q16740, endopeptidase Clp #2: Chemical | ChemComp-FJT / ~{ #3: Chemical | ChemComp-EDO / #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 grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: magnesium chloride, MES, PEG4000 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Dec 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 3.089→42.34 Å / Num. obs: 51326 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.1975 / Rpim(I) all: 0.1277 / Rrim(I) all: 0.236 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.089→3.189 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.143 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 4938 / CC1/2: 0.365 / Rpim(I) all: 0.7334 / Rrim(I) all: 1.362 / % possible all: 95.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.089→42.34 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 3.089→42.34 Å
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