[English] 日本語
Yorodumi- PDB-4wwy: human cationic trypsin G193R mutant in complex with bovine pancre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wwy | ||||||
---|---|---|---|---|---|---|---|
Title | human cationic trypsin G193R mutant in complex with bovine pancreatic trypsin inhibitor | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / trypsin inhibitors / complex / BPTI / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / Activation of Matrix Metalloproteinases ...Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / trypsin / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / collagen-containing extracellular matrix / protease binding / blood microparticle / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Alloy, A. / Kayode, O. / Soares, A.S. / Wang, R. / Radisky, E.S. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Mesotrypsin Has Evolved Four Unique Residues to Cleave Trypsin Inhibitors as Substrates. Authors: Alloy, A.P. / Kayode, O. / Wang, R. / Hockla, A. / Soares, A.S. / Radisky, E.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wwy.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wwy.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 4wwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/4wwy ftp://data.pdbj.org/pub/pdb/validation_reports/ww/4wwy | HTTPS FTP |
---|
-Related structure data
Related structure data | 4wxvC 2ra3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24218.297 Da / Num. of mol.: 2 / Fragment: UNP residues 24-247 / Mutation: G193R, R117H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Organ: pancreas / Plasmid: pTRAP-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07477, trypsin #2: Protein | Mass: 6527.568 Da / Num. of mol.: 2 / Fragment: UNP residues 36-93 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Organ: Pancreas / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P00974 #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M ammonium sulfate, 0.1M sodium cacodylate trihydrate, 30% PEG-8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Feb 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.29 Å / Num. obs: 59179 / % possible obs: 89.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17 |
Reflection shell | Highest resolution: 1.7 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.21 / % possible all: 45.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RA3 Resolution: 1.7→47.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.13 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.31 Å2 / Biso mean: 19.323 Å2 / Biso min: 5.01 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→47.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20
|