+Open data
-Basic information
Entry | Database: PDB / ID: 1k86 | ||||||
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Title | Crystal structure of caspase-7 | ||||||
Components | caspase-7Caspase 7 | ||||||
Keywords | APOPTOSIS / caspase / activation / zymogen | ||||||
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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process ...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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / response to UV / striated muscle cell differentiation / protein catabolic process / protein processing / heart development / peptidase activity / neuron apoptotic process / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Chai, J. / Wu, Q. / Shiozaki, E. / Srinivasa, S.M. / Alnemri, E.S. / Shi, Y. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Crystal structure of a procaspase-7 zymogen: mechanisms of activation and substrate binding Authors: Chai, J. / Wu, Q. / Shiozaki, E. / Srinivasula, S.M. / Alnemri, E.S. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k86.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k86.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k86 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k86 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28769.732 Da / Num. of mol.: 2 / Mutation: C186A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: caspase-7 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P55210, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: 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: 3.69 Å3/Da / Density % sol: 66.67 % | ||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 4000, sodium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||
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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jul 26, 2001 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99 Å / Num. all: 26333 / Num. obs: 23989 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.6→2.69 Å / Num. unique all: 2562 |
Reflection | *PLUS Highest resolution: 2.6 Å / % possible obs: 89.2 % / Num. measured all: 150937 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS Rmerge(I) obs: 0.18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / σ(F): 0.5 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.64 Å / Rfactor Rfree error: 0.012
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0.5 / % reflection Rfree: 5 % / Rfactor obs: 0.232 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.6 Å / Rfactor Rfree: 0.43 / Rfactor Rwork: 0.35 |