+Open data
-Basic information
Entry | Database: PDB / ID: 2p0r | ||||||
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Title | Structure of Human Calpain 9 in complex with Leupeptin | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / inhibitor complex / alpha-beta protein / Hydrolase / calcium-dependent enzyme / Structural Genomics / Structural Genomics Consortium / SGC / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information calcium-dependent cysteine-type endopeptidase activity / digestion / Degradation of the extracellular matrix / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / calcium ion binding / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Actinomycetes Streptomyces roseus MA 839-A1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Davis, T.L. / Paramanathan, R. / Walker, J.R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Davis, T.L. / Paramanathan, R. / Walker, J.R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Structures of Human Minicalpains bound to Inhibitors Authors: Davis, T.L. / Paramanathan, R. / Walker, J.R. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / 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 | 2p0r.cif.gz | 148.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p0r.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 2p0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p0r_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 2p0r_full_validation.pdf.gz | 466.3 KB | Display | |
Data in XML | 2p0r_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 2p0r_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/2p0r ftp://data.pdbj.org/pub/pdb/validation_reports/p0/2p0r | HTTPS FTP |
-Related structure data
Related structure data | 1nqaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | One molecule of the asymmetric unit is the biological assembly |
-Components
#1: Protein | Mass: 37527.973 Da / Num. of mol.: 2 / Fragment: minicalpain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAPN9, NCL4 / Plasmid: pET28-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: O14815, calpain-1 #2: Protein/peptide | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Compound details | THE LEUPEPTIN IS SUPPOSED TO BE COVALENTLY CONNECTED TO ACTIVE_SITE CYS 97 OF THE ENZYME TO FORM A ...THE LEUPEPTIN IS SUPPOSED TO BE 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 | |
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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: 2.69 Å3/Da / Density % sol: 54.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 14.7% Peg 8000, 10% glycerol, 0.1M Na-Cacodylate, 0.15M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 33145 / Num. obs: 33145 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 9.1 % / Biso Wilson estimate: 53.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.646 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NQA Resolution: 2.5→19.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.536 / SU ML: 0.226 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.501 / ESU R Free: 0.302 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.859 Å2
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Refine analyze | Luzzati coordinate error obs: 0.372 Å / Luzzati d res low obs: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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