+Open data
-Basic information
Entry | Database: PDB / ID: 6nry | ||||||
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Title | Crystal structure of human caspase-4 | ||||||
Components | Caspase-4Caspase 4 | ||||||
Keywords | IMMUNE SYSTEM / inflammation / caspase / pyroptosis / enzyme | ||||||
Function / homology | Function and homology information caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / canonical inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / pyroptotic inflammatory response / protein maturation ...caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / canonical inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / pyroptotic inflammatory response / protein maturation / protein autoprocessing / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / intrinsic apoptotic signaling pathway / lipopolysaccharide binding / NOD1/2 Signaling Pathway / positive regulation of inflammatory response / cellular response to amyloid-beta / regulation of inflammatory response / regulation of apoptotic process / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / cysteine-type endopeptidase activity / innate immune response / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.184 Å | ||||||
Authors | Yang, J. / Liu, Z. / Shi, W. / Xiao, T.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human caspase-4 Authors: Yang, J. / Liu, Z. / Xiao, T.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nry.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nry.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 6nry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/6nry ftp://data.pdbj.org/pub/pdb/validation_reports/nr/6nry | HTTPS FTP |
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-Related structure data
Related structure data | 3e4cS 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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-Components
#1: Protein | Mass: 32826.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P49662, caspase-4 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25mM Bis-Tris, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→27.6 Å / Num. obs: 18369 / % possible obs: 99.3 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rrim(I) all: 0.056 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.876 / Rrim(I) all: 0.752 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3e4c Resolution: 2.184→27.592 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.184→27.592 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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