[English] 日本語
Yorodumi- PDB-1aks: CRYSTAL STRUCTURE OF THE FIRST ACTIVE AUTOLYSATE FORM OF THE PORC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aks | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE FIRST ACTIVE AUTOLYSATE FORM OF THE PORCINE ALPHA TRYPSIN | ||||||
Components | (ALPHA TRYPSIN) x 2 | ||||||
Keywords | SERINE PROTEASE / HYDROLASE | ||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Johnson, A. / Krishnaswamy, S. / Sundaram, P.V. / Pattabhi, V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: The first structure at 1.8 A resolution of an active autolysate form of porcine alpha-trysoin. Authors: Johnson, A. / Krishnaswamy, S. / Sundaram, P.V. / Pattabhi, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1aks.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1aks.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 1aks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aks_validation.pdf.gz | 420.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1aks_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 1aks_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 1aks_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1aks ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1aks | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13303.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00761, trypsin |
---|---|
#2: Protein | Mass: 10205.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00761, trypsin |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | THE 223 AMINO ACIDS OF TRYPSIN ARE IDENTIFIED BY THE RESIDUE NUMBERS OF THE HOMOLOGOUS ...THE 223 AMINO ACIDS OF TRYPSIN ARE IDENTIFIED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.23 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 293 K / pH: 6.7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. obs: 17486 / % possible obs: 95 % / Num. measured all: 56502 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 91.3 % / Num. unique obs: 4585 / Num. measured obs: 15077 / Rmerge(I) obs: 0.661 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→8 Å / σ(F): 1 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 2 Å / Rfactor Rfree: 0.31 / Rfactor obs: 0.27 |