+Open data
-Basic information
Entry | Database: PDB / ID: 1ezu | ||||||
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Title | ECOTIN Y69F, D70P BOUND TO D102N TRYPSIN | ||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / macromolecular complex / protease inhibitor / protein-protein interactions / HYDROLASE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase inhibitor activity ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Collagen degradation / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / serine-type endopeptidase inhibitor activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / calcium ion binding / protein homodimerization activity / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Gillmor, S.A. / Takeuchi, T. / Yang, S.Q. / Craik, C.S. / Fletterick, R.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Compromise and accommodation in ecotin, a dimeric macromolecular inhibitor of serine proteases. Authors: Gillmor, S.A. / Takeuchi, T. / Yang, S.Q. / Craik, C.S. / Fletterick, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ezu.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ezu.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ezu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/1ezu ftp://data.pdbj.org/pub/pdb/validation_reports/ez/1ezu | 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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Details | The biologically relevant assembly is the same two-ecotin, two trypsin hetero tetramer forming the asymmetric unit |
-Components
#1: Protein | Mass: 16086.534 Da / Num. of mol.: 2 / Mutation: Y69F, D70P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTACTACECOTIN / Production host: Escherichia coli (E. coli) / References: UniProt: P23827 #2: Protein | Mass: 23814.840 Da / Num. of mol.: 2 / Mutation: D102N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: PANCREAS / Plasmid: PYTD102N TRYPSIN / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00763, trypsin #3: Chemical | #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: 2.64 Å3/Da / Density % sol: 53.48 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: protein: 15mg/ml in 10mM Tris pH 8.0 well: 16.5% Peg 4k, 0.15 M Sodium Cacodylate, 0.3M Sodium Acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 18, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 30337 / Num. obs: 30337 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.346 / Num. unique all: 2724 / % possible all: 84.1 |
Reflection | *PLUS Num. measured all: 89735 |
Reflection shell | *PLUS % possible obs: 84.1 % |
-Processing
Software |
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Refinement | Resolution: 2.4→25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: used bulk solvent correction, b factor refinement, positional refinement, and simulated annealing
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Displacement parameters | Biso mean: 44.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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