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Yorodumi- PDB-3i2x: Crystal structure of a chimeric trypsin inhibitor having reactive... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i2x | ||||||
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Title | Crystal structure of a chimeric trypsin inhibitor having reactive site loop of ETI on the scaffold of WCI | ||||||
Components | Chymotrypsin inhibitor 3 | ||||||
Keywords | HYDROLASE INHIBITOR / ETI(L)-WCI(S) / MUTANT / TRYPSIN INHIBITOR / CHIMERIC PROTEIN / SERINE PROTEASE INHIBITOR / HYDROLASE/HYDROLASE INHIBITOR / Disulfide bond / Protease inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Psophocarpus tetragonolobus (winged bean) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Sen, U. / Khamrui, S. / Dasgupta, J. / Dattagupta, J.K. / Majumder, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Identification of a novel set of scaffolding residues that are instrumental for the inhibitory property of Kunitz (STI) inhibitors. Authors: Khamrui, S. / Majumder, S. / Dasgupta, J. / Dattagupta, J.K. / Sen, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i2x.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i2x.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/3i2x ftp://data.pdbj.org/pub/pdb/validation_reports/i2/3i2x | HTTPS FTP |
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-Related structure data
Related structure data | 3i2aC 1eylS C: citing same article (ref.) 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
#1: Protein | Mass: 20677.326 Da / Num. of mol.: 2 / Mutation: Q66P, F67L, L68R, L70A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psophocarpus tetragonolobus (winged bean) Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10822 #2: 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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. obs: 7552 / Redundancy: 2.35 % / Biso Wilson estimate: 1.5 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 2.35 |
-Processing
Software | Name: CNS / Version: 1.2 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EYL Resolution: 2.85→19.87 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1179908.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.23 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→19.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
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Xplor file |
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