+Open data
-Basic information
Entry | Database: PDB / ID: 2ary | ||||||
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Title | Catalytic domain of Human Calpain-1 | ||||||
Components | Calpain-1 catalytic subunit | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEASE / PAPAIN / CALCIUM-DEPENDENT / THIOL PROTEASE / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information calpain-1 / calpain complex / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / Formation of the cornified envelope / self proteolysis / cornified envelope / regulation of catalytic activity / regulation of NMDA receptor activity ...calpain-1 / calpain complex / mammary gland involution / calcium-dependent cysteine-type endopeptidase activity / receptor catabolic process / Formation of the cornified envelope / self proteolysis / cornified envelope / regulation of catalytic activity / regulation of NMDA receptor activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / peptidase activity / ficolin-1-rich granule lumen / lysosome / focal adhesion / calcium ion binding / positive regulation of cell population proliferation / Neutrophil degranulation / mitochondrion / proteolysis / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Walker, J.R. / Davis, T. / Lunin, V. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Davis, T. / Lunin, V. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Crystal Structures of Human Calpains 1 and 9 Imply Diverse Mechanisms of Action and Auto-inhibition Authors: Davis, T.L. / Walker, J.R. / Finerty, P.J. / Mackenzie, F. / Newman, E.M. / Dhe-Paganon, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ary.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ary.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 2ary.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ary_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
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Full document | 2ary_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 2ary_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 2ary_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/2ary ftp://data.pdbj.org/pub/pdb/validation_reports/ar/2ary | HTTPS FTP |
-Related structure data
Related structure data | 1zivC 1tloS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 39578.465 Da / Num. of mol.: 2 / Fragment: Catalytic domain, residues 33-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN1, CANPL1 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07384, calpain-1 #2: Chemical | ChemComp-CA / #3: Chemical | #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: 3.39 Å3/Da / Density % sol: 63.42 % |
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Crystal grow | Temperature: 298 K / pH: 7.75 Details: 1.5 M Ammononium Formate, 0.1 M Tris pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97889 |
Detector | Type: SBC-3 / Detector: CCD / Date: Aug 13, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97889 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.32 Å / Num. obs: 42153 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.56 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.44 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TLO Resolution: 2.4→44.32 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.352 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.488 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→44.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.463 Å / Total num. of bins used: 20
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