+Open data
-Basic information
Entry | Database: PDB / ID: 5k20 | ||||||
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Title | Caspase-7 S239E Phosphomimetic | ||||||
Components |
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Keywords | HYDROLASE / protease / phosphomimetic / PAK2 / phosphorylation | ||||||
Function / homology | Function and homology information caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Eron, S.J. / Hardy, J.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: PAK2 Phosphorylation Inhibits Caspase-7 by Two Divergent Mechanisms: Slowing Activation and Blocking Substrate Binding Authors: Eron, S.J. / Hardy, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k20.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k20.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 5k20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k20_validation.pdf.gz | 472 KB | Display | wwPDB validaton report |
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Full document | 5k20_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 5k20_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5k20_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/5k20 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/5k20 | HTTPS FTP |
-Related structure data
Related structure data | 3ibfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | tetramer according to gel filtration, mass spectrometry, gel electroporesis, literature reports. This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303). |
-Components
#1: Protein | Mass: 22189.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This ...Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303). The large subunit of caspase-7 crystallized here consisted of residues 24-198. Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P55210, caspase-7 #2: Protein | Mass: 13265.836 Da / Num. of mol.: 2 / Mutation: S272E Source method: isolated from a genetically manipulated source Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This ...Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303). The small subunit of caspase-7 crystallized here consisted of residues 206-303 (including a 6xHis tag). Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55210, caspase-7 #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: 3.07 Å3/Da / Density % sol: 59.87 % / Description: Rhomboids of 240 x 340 microns |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.1 M Sodium Formate 100 mM Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→76.98 Å / Num. obs: 43569 / % possible obs: 99.53 % / Redundancy: 10.9 % / Biso Wilson estimate: 66.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IBF Resolution: 2.2→76.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 12.25 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.162 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.17 Å2 / Biso mean: 66.342 Å2 / Biso min: 40.01 Å2
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Refinement step | Cycle: final / Resolution: 2.2→76.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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