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Open data
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Basic information
Entry | Database: PDB / ID: 1fi8 | ||||||
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Title | RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD] | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / complex (serine protease-inhibitor) / protease substrate interactions / beta strand structure / chymotrypsin fold / granzyme B / ecotin / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() Activation, myristolyation of BID and translocation to mitochondria / granzyme B / granzyme-mediated apoptotic signaling pathway / : / cytolytic granule / cytolysis / positive regulation of necroptotic process / natural killer cell mediated cytotoxicity / serine-type peptidase activity / serine-type endopeptidase inhibitor activity ...Activation, myristolyation of BID and translocation to mitochondria / granzyme B / granzyme-mediated apoptotic signaling pathway / : / cytolytic granule / cytolysis / positive regulation of necroptotic process / natural killer cell mediated cytotoxicity / serine-type peptidase activity / serine-type endopeptidase inhibitor activity / T cell mediated cytotoxicity / defense response / outer membrane-bounded periplasmic space / early endosome / negative regulation of translation / serine-type endopeptidase activity / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Waugh, S.M. / Harris, J.L. / Fletterick, R.J. / Craik, C.S. | ||||||
![]() | ![]() Title: The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity Authors: Waugh, S.M. / Harris, J.L. / Fletterick, R. / Craik, C.S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.3 KB | Display | ![]() |
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PDB format | ![]() | 120.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | the biological assembly is the tetramer in the asymmetric unit. |
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Components
#1: Protein | Mass: 25225.396 Da / Num. of mol.: 2 / Mutation: N66Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P18291, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein | Mass: 9528.733 Da / Num. of mol.: 2 / Fragment: RESIDUES 28 - 111 / Mutation: V81I, S82E, T83P, M84D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 6645.746 Da / Num. of mol.: 2 / Fragment: RESIDUES 112 - 169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 49.15 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: sodium acetate, PEGmme 2000, ammonium acetate,, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 5.8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.2→35.8 Å / Num. all: 98218 / Num. obs: 98218 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.8 | |||||||||||||||
Reflection shell | Resolution: 2.21→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.58 / Num. unique all: 48837 / % possible all: 90.7 | |||||||||||||||
Reflection | *PLUS Num. obs: 48837 / Num. measured all: 121975 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 90 % |
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Processing
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Refinement | Resolution: 2.2→35.7 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber Details: Crystal 1 data was used for initial molecular replacement and refinement. Crystal 2 data was given the same Rfree set and used for final refinement. Molecular replacement used 1AZZ and 1AUG.
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Displacement parameters | Biso mean: 43.09 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→35.7 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 35.7 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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