[English] 日本語
Yorodumi- PDB-1d6r: CRYSTAL STRUCTURE OF CANCER CHEMOPREVENTIVE BOWMAN-BIRK INHIBITOR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d6r | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF CANCER CHEMOPREVENTIVE BOWMAN-BIRK INHIBITOR IN TERNARY COMPLEX WITH BOVINE TRYPSIN AT 2.3 A RESOLUTION. STRUCTURAL BASIS OF JANUS-FACED SERINE PROTEASE INHIBITOR SPECIFICITY | ||||||
Components |
| ||||||
Keywords | HYDROLASE / PROTEASE INHIBITOR / SERINE PROTEASE / BOWMAN-BIRK INHIBITOR | ||||||
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 / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Glycine max (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Koepke, J. / Ermler, U. / Wenzl, G. / Flecker, P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of cancer chemopreventive Bowman-Birk inhibitor in ternary complex with bovine trypsin at 2.3 A resolution. Structural basis of Janus-faced serine protease inhibitor specificity. Authors: Koepke, J. / Ermler, U. / Warkentin, E. / Wenzl, G. / Flecker, P. #1: Journal: Eur.J.Biochem. / Year: 1996 Title: Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution-structural peculiarities in a folded protein conformation. Authors: Voss, R.H. / Ermler, U. / Essen, L.O. / Wenzl, G. / Kim, Y.M. / Flecker, P. #2: Journal: Eur.J.Biochem. / Year: 1987 Title: Chemical synthesis, molecular cloning and expression of gene coding for a Bowman-Birk-type proteinase inhibitor Authors: Flecker, P. #3: Journal: J.Biochem.Biophys.Methods / Year: 1996 Title: Proteolytic cleavage of soybean Bowman-Birk inhibitor monitored by means of high-performance capillary electrophoresis Authors: Jensen, B. / Unger, K.K. / Uebe, J. / Gey, M. / Kim, Y.M. / Flecker, P. #4: Journal: FEBS Lett. / Year: 1989 Title: A new and general procedure for refolding mutant Bowman-Birk-type proteinase inhibitors on trypsin-Sepharose as a matrix with complementary structure Authors: Flecker, P. #5: Journal: Eur.J.Biochem. / Year: 1995 Title: Template-directed protein folding into a metastable state of increased activity Authors: Flecker, P. #6: Journal: Eur.J.Biochem. / Year: 1998 Title: Mutational analysis of disulfide bonds in the trypsin-reactive subdomain of a Bowman-Birk-type inhibitor of trypsin and chymotrypsin. Cooperative versus autonomous refolding of subdomains. Authors: Philipp, S. / Kim, Y.M. / Durr, I. / Wenzl, G. / Vogt, M. / Flecker, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1d6r.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1d6r.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 1d6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/1d6r ftp://data.pdbj.org/pub/pdb/validation_reports/d6/1d6r | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Fragment: CATIONIC PRECURSOR / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: ACINAR CELL / Organ: PANCREAS / References: UniProt: P00760, trypsin |
---|---|
#2: Protein | Mass: 6431.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / References: UniProt: P01055 |
#3: Water | ChemComp-HOH / |
Compound details | TRIPLE-STRANDED B-HAIRPIN MOTIF OF BOWMAN-BIRK PROTEASE INHIBITOR INTERACTS WITH SURFACE LOOPS ...TRIPLE-STRANDED B-HAIRPIN MOTIF OF BOWMAN-BIRK PROTEASE INHIBITOR INTERACTS WITH SURFACE LOOPS SURROUNDIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.33 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PROTEIN SOLUTION: TRIS/CL, CACL2, MGSO4.7H2O, NAN3 PLUS PRECIPITANT PRECIPITANTS: (NH4)2SO4, MDP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 5, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→10 Å / Num. all: 54604 / Num. obs: 54604 / % possible obs: 82.3 % / Observed criterion σ(F): 0.01 / Observed criterion σ(I): 0.01 / Redundancy: 4.838 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.3→2.4 Å / % possible all: 60.9 |
Reflection | *PLUS Num. obs: 18001 / Num. measured all: 54604 |
Reflection shell | *PLUS % possible obs: 60.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.3→8 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|