[English] 日本語
Yorodumi- PDB-2tbs: COLD-ADAPTION OF ENZYMES: STRUCTURAL COMPARISON BETWEEN SALMON AN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2tbs | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | COLD-ADAPTION OF ENZYMES: STRUCTURAL COMPARISON BETWEEN SALMON AND BOVINE TRYPSINS | |||||||||
Components | TRYPSIN | |||||||||
Keywords | HYDROLASE(SERINE PROTEINASE) | |||||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Salmo salar (Atlantic salmon) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Smalas, A.O. | |||||||||
Citation | Journal: Proteins / Year: 1994 Title: Cold adaption of enzymes: structural comparison between salmon and bovine trypsins. Authors: Smalas, A.O. / Heimstad, E.S. / Hordvik, A. / Willassen, N.P. / Male, R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar) Authors: Smalas, A.O. / Hordvik, A. #2: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallization and Preliminary X-Ray Crystallographic Studies of Benzamidine-Inhibited Trypsin from the North Atlantic Salmon (Salmo Salar) Authors: Smalas, A.O. / Hordvik, A. / Hansen, L.K. / Hough, E. / Jynge, K. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1983 Title: The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors Authors: Marquart, M. / Walter, J. / Deisenhofer, J. / Bode, W. / Huber, R. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2tbs.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2tbs.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 2tbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tbs_validation.pdf.gz | 414.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2tbs_full_validation.pdf.gz | 474.8 KB | Display | |
Data in XML | 2tbs_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2tbs_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/2tbs ftp://data.pdbj.org/pub/pdb/validation_reports/tb/2tbs | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23784.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmo salar (Atlantic salmon) / References: UniProt: P35031, trypsin |
---|---|
#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-BEN / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THE CALCIUM IS ION IS BOUND IN A MANNER SIMILAR TO THAT OBSERVED IN BOVINE TRYPSIN. |
Sequence details | THE AMINO ACID NUMBERING SCHEME USED IS ADOPTED FROM CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.7 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 28-30 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→6 Å / Num. reflection obs: 14474 / σ(F): 3 Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT METHODS, USING THE MERLOT-PACKAGE (FITZGERALD, P. (1988) J.APPL. CRYST., 21, 273-278), AND THE REFINED MODEL OF BOVINE TRYPSIN AS SEARCH ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT METHODS, USING THE MERLOT-PACKAGE (FITZGERALD, P. (1988) J.APPL. CRYST., 21, 273-278), AND THE REFINED MODEL OF BOVINE TRYPSIN AS SEARCH MODEL (PROTEIN DATA BANK, ENTRY 3PTB). THIS ENTRY WAS REFINED USING A NON-STANDARD SETTING FOR THE SPACE GROUP P 21 21 2. THE FOLLOWING SYMMETRY OPERATORS MUST BE USED TO GENERATE CRYSTALLOGRAPHICALLY RELATED MOLECULES. X, Y, Z -X, 1/2+Y, -Z 1/2+X, -Y, -Z 1/2-X, 1/2-Y, Z | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.165 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |