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Yorodumi- PDB-1avx: COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, TET... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1avx | ||||||
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Title | COMPLEX PORCINE PANCREATIC TRYPSIN/SOYBEAN TRYPSIN INHIBITOR, TETRAGONAL CRYSTAL FORM | ||||||
Components |
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Keywords | COMPLEX (PROTEINASE/INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) / PORCINE TRYPSIN / SOYBEAN TRYPSIN INHIBITOR / KUNITZ-TYPE / BETA-TREFOIL FOLD / COMPLEX (PROTEINASE-INHIBITOR) complex | ||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Song, H.K. / Suh, S.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Kunitz-type soybean trypsin inhibitor revisited: refined structure of its complex with porcine trypsin reveals an insight into the interaction between a homologous inhibitor from Erythrina ...Title: Kunitz-type soybean trypsin inhibitor revisited: refined structure of its complex with porcine trypsin reveals an insight into the interaction between a homologous inhibitor from Erythrina caffra and tissue-type plasminogen activator. Authors: Song, H.K. / Suh, S.W. #1: Journal: Thesis, Seoul National University / Year: 1997 Title: Crystal Structure Analyses of Human A1-Antitrypsin, Soybean Kunitz-Type Trypsin Inhibitor, and Barley Chitinase Authors: Song, H.K. #2: Journal: Mol.Cells / Year: 1993 Title: Crystallization of Kunitz-Type Soybean Trypsin Inhibitor Authors: Lee, J.K. / Song, H.K. / Hwang, K.Y. / Kim, K.K. / Suh, S.W. #3: Journal: Thesis, Seoul National University / Year: 1993 Title: Crystallization and Preliminary X-Ray Crystallographic Study of Kunitz-Type Soybean Trypsin Inhibitor Authors: Lee, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1avx.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1avx.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 1avx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1avx_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 1avx_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 1avx_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1avx_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/1avx ftp://data.pdbj.org/pub/pdb/validation_reports/av/1avx | HTTPS FTP |
-Related structure data
Related structure data | 1avuC 1avwC 1mctS 1tieS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00761, trypsin |
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#2: Protein | Mass: 19657.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Organ: SEED / References: UniProt: P01070 |
#3: Chemical | ChemComp-CA / |
#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: 2.56 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 5.68 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→60 Å / Num. obs: 26956 / % possible obs: 62 % / Observed criterion σ(I): 0.5 / Redundancy: 5.2 % / Rmerge(I) obs: 0.079 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 37.2 |
Reflection | *PLUS Num. measured all: 118553 |
Reflection shell | *PLUS % possible obs: 37.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MCT FOR TRYPSIN AND PDB ENTRY 1TIE FOR THE INHIBITOR Resolution: 1.9→8 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / σ(F): 2
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Refine analyze | Luzzati d res low obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |