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Yorodumi- PDB-1mdw: Crystal Structure of Calcium-Bound Protease Core of Calpain II Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mdw | ||||||
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Title | Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis for Intrinsic Inactivation | ||||||
Components | Calpain II, catalytic subunit | ||||||
Keywords | HYDROLASE / Calpain Cysteine Protease Fold / Two Cooperative Calcium Sites / Helix Instability / Tryptophan-Based Active Site Blockage | ||||||
Function / homology | Function and homology information calpain-2 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / positive regulation of cardiac muscle cell apoptotic process ...calpain-2 / Degradation of the extracellular matrix / positive regulation of phosphatidylcholine biosynthetic process / calpain complex / calcium-dependent cysteine-type endopeptidase activity / perinuclear endoplasmic reticulum / myoblast fusion / regulation of interleukin-6 production / positive regulation of myoblast fusion / positive regulation of cardiac muscle cell apoptotic process / behavioral response to pain / pseudopodium / blastocyst development / protein autoprocessing / cellular response to interferon-beta / response to mechanical stimulus / cytoskeletal protein binding / cellular response to amino acid stimulus / proteolysis involved in protein catabolic process / cell projection / female pregnancy / protein catabolic process / response to hydrogen peroxide / peptidase activity / cellular response to lipopolysaccharide / lysosome / response to hypoxia / membrane raft / external side of plasma membrane / focal adhesion / neuronal cell body / dendrite / calcium ion binding / chromatin / protein-containing complex binding / enzyme binding / Golgi apparatus / endoplasmic reticulum / proteolysis / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Jia, Z. / Davies, P.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Calpain silencing by a reversible intrinsic mechanism. Authors: Moldoveanu, T. / Hosfield, C.M. / Lim, D. / Jia, Z. / Davies, P.L. #1: Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: A Ca(2+) 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: Embo J. / Year: 1999 Title: Crystal Structure of Calpain Reveals the Structural Basis for Ca(2+)-dependent Protease Activity and a Novel Mode of Enzyme Activation Authors: Hosfield, C.M. / Elce, J.S. / Davies, P.L. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mdw.cif.gz | 145.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mdw.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mdw_validation.pdf.gz | 434.2 KB | Display | wwPDB validaton report |
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Full document | 1mdw_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 1mdw_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 1mdw_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/1mdw ftp://data.pdbj.org/pub/pdb/validation_reports/md/1mdw | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is the monomer of the dimer in the assymetric unit |
-Components
#1: Protein | Mass: 36807.980 Da / Num. of mol.: 2 / Fragment: Protease Core Domains I and II (Residues 17-346) / Mutation: C105S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CALPAIN II / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q07009, EC: 3.4.22.17 #2: Chemical | ChemComp-CA / #3: 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: 2.5 Å3/Da / Density % sol: 50.88 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10% PEG6000, 0.1M Sodium Acetate, 30mM calcium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 7, 2001 / Details: Mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 48591 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.049 / Rsym value: 0.035 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.95→2.05 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4424 / Rsym value: 0.326 / % possible all: 89.9 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 496583 |
Reflection shell | *PLUS % possible obs: 89.9 % / Num. unique obs: 4424 / Num. measured obs: 14861 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |