+Open data
-Basic information
Entry | Database: PDB / ID: 5ic6 | ||||||
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Title | Crystal structure of caspase-7 DEVE peptide complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / apoptosis / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / heart development / peptidase activity / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / neuron apoptotic process / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Seaman, J.E. / Julien, O. / Lee, P.S. / Rettenmaier, T.J. / Thomsen, N.D. / Wells, J.A. | ||||||
Citation | Journal: Cell Death Differ. / Year: 2016 Title: Cacidases: caspases can cleave after aspartate, glutamate and phosphoserine residues. Authors: Seaman, J.E. / Julien, O. / Lee, P.S. / Rettenmaier, T.J. / Thomsen, N.D. / Wells, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ic6.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ic6.ent.gz | 160.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ic6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ic6_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 5ic6_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 5ic6_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 5ic6_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/5ic6 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/5ic6 | HTTPS FTP |
-Related structure data
Related structure data | 5ic4C 2ql5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22189.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7 #2: Protein | Mass: 13223.800 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7 #3: Protein/peptide | Mass: 488.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M ammonium fluoride, 0.1 M sodium acetate pH 4.6, 20% (w/v) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115856 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115856 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 17178 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.7 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QL5 Resolution: 2.7→47.15 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→47.15 Å
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Refine LS restraints |
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LS refinement shell |
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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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