[English] 日本語
Yorodumi- PDB-1tlo: High resolution crystal structure of calpain I protease core in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tlo | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution crystal structure of calpain I protease core in complex with E64 | ||||||
Components | Calpain 1, large [catalytic] subunit | ||||||
Keywords | HYDROLASE / covalently-linked inhibitor at the active site (cysteine 115) forms a thioester | ||||||
Function / homology | Function and homology information calpain-1 / Degradation of the extracellular matrix / mammary gland involution / positive regulation of leukocyte tethering or rolling / 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 / mammary gland involution / positive regulation of leukocyte tethering or rolling / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1tlo.cif.gz | 82 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1tlo.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tlo_validation.pdf.gz | 725.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1tlo_full_validation.pdf.gz | 735.6 KB | Display | |
Data in XML | 1tlo_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1tlo_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/1tlo ftp://data.pdbj.org/pub/pdb/validation_reports/tl/1tlo | HTTPS FTP |
-Related structure data
Related structure data | 1tl9C 1kxrS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-E64 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.01 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: sodium chloride, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 100K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.937 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.937 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 24647 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.077 / Rsym value: 0.067 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 6 / Num. unique all: 2417 / Rsym value: 0.292 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1KXR Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
| ||||||||||||||||||||
Refine LS restraints |
|