+Open data
-Basic information
Entry | Database: PDB / ID: 1m72 | ||||||
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Title | Crystal Structure of Caspase-1 from Spodoptera frugiperda | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / CASPASE / CYSTEINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of neuron apoptotic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Spodoptera frugiperda (fall armyworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Forsyth, C.M. / Lemongello, D. / Friesen, P.D. / Fisher, A.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structure of an invertebrate caspase. Authors: Forsyth, C.M. / Lemongello, D. / LaCount, D.J. / Friesen, P.D. / Fisher, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m72.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m72.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m72_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 1m72_full_validation.pdf.gz | 492.9 KB | Display | |
Data in XML | 1m72_validation.xml.gz | 33.5 KB | Display | |
Data in CIF | 1m72_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m72 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m72 | HTTPS FTP |
-Related structure data
Related structure data | 1cp3S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Biological assembly is dimer of dimers. Chains A and B make up one biological assembly unit. Chain C and its crystallographic 2-fold (x-y,-y,-z+1/3) related chain make up another biological assembly. |
-Components
#1: Protein | Mass: 30763.057 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P89116, caspase-1 #2: Protein/peptide | #3: Chemical | ChemComp-EDO / #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: 2.81 Å3/Da / Density % sol: 56.29 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6M Ammonium Sulfate, 2% PEG 1000, 0.1M sodium HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2002 / Details: 16 pole wiggler |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 45896 / Num. obs: 45896 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.94 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3 / Num. unique all: 3012 / Rsym value: 0.265 / % possible all: 97.2 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 45879 / % possible obs: 97.6 % / Num. measured all: 100942 |
Reflection shell | *PLUS % possible obs: 97 % / Mean I/σ(I) obs: 2.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CP3 Resolution: 2.3→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2395527.33 / Data cutoff high rms absF: 2395527.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.3924 Å2 / ksol: 0.356485 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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