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Yorodumi- PDB-1tl9: High resolution crystal structure of calpain I protease core in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tl9 | ||||||
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Title | High resolution crystal structure of calpain I protease core in complex with leupeptin | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Covalently-linked inhibitor at the active site cysteine forms a hemithioacetal / hydrolase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information calpain-1 / Degradation of the extracellular matrix / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / negative regulation of actin filament polymerization / self proteolysis / cornified envelope / regulation of catalytic activity ...calpain-1 / Degradation of the extracellular matrix / positive regulation of leukocyte tethering or rolling / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / negative regulation of actin filament polymerization / self proteolysis / cornified envelope / regulation of catalytic activity / positive regulation of vascular permeability / response to arsenic-containing substance / response to angiotensin / negative regulation of non-canonical NF-kappaB signal transduction / Neutrophil degranulation / positive regulation of cardiac muscle cell apoptotic process / protein autoprocessing / cytoskeletal protein binding / protein catabolic process / cellular response to hydrogen peroxide / peptidase activity / lysosome / calcium ion binding / enzyme binding / mitochondrion / proteolysis / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Actinomycetes Streptomyces roseus MA 839-A1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Moldoveanu, T. / Campbell, R.L. / Cuerrier, D. / Davies, P.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal Structures of Calpain-E64 and -Leupeptin Inhibitor Complexes Reveal Mobile Loops Gating the Active Site Authors: Moldoveanu, T. / Campbell, R.L. / Cuerrier, D. / Davies, P.L. #1: Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: A calcium switch aligns the active site of calpain Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Elce, J.S. / Jia, Z. / Davies, P.L. #2: Journal: Nat.Struct.Mol.Biol. / Year: 2003 Title: calpain silencing by a reversible intrinsic mechanism Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Jia, Z. / Davies, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tl9.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tl9.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1tl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/1tl9 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/1tl9 | HTTPS FTP |
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-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: 38804.551 Da / Num. of mol.: 1 / Fragment: residues 27-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CAPN1, CLS1 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P97571, calpain-1 | ||||||
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#2: Protein/peptide | | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE LEUPEPTIN IS COVALENTLY | Sequence details | THERE IS A DISCREPANCY IN THE NORINE AND PDB NUMBERING, AS NORINE COUNTS ACE AND LEU TOGETHER AS ...THERE IS A DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | pH: 6 Details: sodium chloride, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 2, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 31962 / % possible obs: 95 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.069 / Rsym value: 0.072 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 14.9 / Num. measured obs: 3221 / Rsym value: 0.152 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KXRB Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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