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Yorodumi- PDB-4j2y: Crystal structure of a plant trypsin inhibitor EcTI in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j2y | |||||||||
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Title | Crystal structure of a plant trypsin inhibitor EcTI in complex with bovine trypsin. | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / trefoil / serine protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Enterolobium contortisiliquum (plant) Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Zhou, D. / Wlodawer, A. | |||||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal Structures of a Plant Trypsin Inhibitor from Enterolobium contortisiliquum (EcTI) and of Its Complex with Bovine Trypsin. Authors: Zhou, D. / Lobo, Y.A. / Batista, I.F. / Marques-Porto, R. / Gustchina, A. / Oliva, M.L. / Wlodawer, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j2y.cif.gz | 164.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j2y.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 4j2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j2y_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 4j2y_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 4j2y_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 4j2y_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/4j2y ftp://data.pdbj.org/pub/pdb/validation_reports/j2/4j2y | HTTPS FTP |
-Related structure data
Related structure data | 4j2kC 1avwS 2bzaS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19866.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterolobium contortisiliquum (plant) / References: UniProt: P86451 |
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#2: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 1.95 Å3/Da / Density % sol: 36.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M ammonium sulfate, 0.1 M Tris pH7.5, 30% PEG1500, 0.2 M LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 22920 / Num. obs: 21100 / % possible obs: 92.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.081 |
Reflection shell | Resolution: 2→2.2 Å / Rmerge(I) obs: 0.396 / Num. unique all: 5639 / % possible all: 80.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AVW AND 2BZA Resolution: 2→19.845 Å / SU ML: 0.34 / Phase error: 27.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.49 Å2 / ksol: 0.374 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→19.845 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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