[English] 日本語
Yorodumi- PDB-1esb: DIRECT STRUCTURE OBSERVATION OF AN ACYL-ENZYME INTERMEDIATE IN TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1esb | ||||||
---|---|---|---|---|---|---|---|
Title | DIRECT STRUCTURE OBSERVATION OF AN ACYL-ENZYME INTERMEDIATE IN THE HYDROLYSIS OF AN ESTER SUBSTRATE BY ELASTASE | ||||||
Components | PORCINE PANCREATIC ELASTASE | ||||||
Keywords | HYDROLASE / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Ding, X. / Rasmussen, B. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 1994 Title: Direct structural observation of an acyl-enzyme intermediate in the hydrolysis of an ester substrate by elastase. Authors: Ding, X. / Rasmussen, B.F. / Petsko, G.A. / Ringe, D. #1: Journal: J.Am.Chem.Soc. / Year: 1989 Title: Crystal Structure of the Covalent Complex Formed by a Peptidyl Alpha,Alpha-Difluoro-Beta-Keto Amide with Porcine Pancreatic Elastase at 1.78 Angstroms Resolution Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfield Junior, R.E. / Meyer Junior, E.F. / Trainor, D.A. #2: Journal: Acta Crystallogr.,Sect.B / Year: 1988 Title: Structure of Native Procine Pancreatic Elastase at 1.65 Angstroms Resolution Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O. #3: Journal: J.Mol.Biol. / Year: 1980 Title: Structures of Product and Inhibitor Complexes of Streptomyces Griseus Protease a at 1.8 Angstroms Resolution Authors: James, M.N.G. / Sielecki, A.R. / Brayer, G.D. / Delbaere, L.T.J. #4: Journal: Nature / Year: 1976 Title: Formation of Stable Crystalline Enzyme-Substrate Intermediates at Sub-Zero Temperatures Authors: Fink, A.L. / Ahmed, A.I. #5: Journal: Nature / Year: 1976 Title: Crystal Structure of Elastase-Substrate Complex at-55 Degc Authors: Alber, T. / Petsko, G.A. / Tsernoglou, D. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* ON SHEET RECORDS BELOW ARE ACTUALLY SIX-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRAND OF EACH SHEET ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1esb.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1esb.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 1esb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1esb ftp://data.pdbj.org/pub/pdb/validation_reports/es/1esb | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase |
---|---|
#2: Chemical | ChemComp-BBL / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | BBL IS COVALENTLY LINKED TO SER 203. THE P-NITROPHENYL GROUP ORIGINALLY PRESENT IN BBL MOLECULE IS ...BBL IS COVALENTLY |
Sequence details | THE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL STARTING WITH VAL 16 AND ENDING WITH ASN ...THE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 5 / Method: unknown / Details: Sawyer, L., (1978) J. Mol. Biol., 118, 137. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 11 Å / Num. all: 10437 / Num. obs: 10437 / % possible obs: 97 % |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.3→10 Å / Rfactor Rwork: 0.21 / Rfactor obs: 0.21 / σ(F): 1 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
| ||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.21 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|