+Open data
-Basic information
Entry | Database: PDB / ID: 1fni | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF PORCINE BETA TRYPSIN WITH 0.01% POLYDOCANOL | ||||||
Components | TRYPSIN | ||||||
Keywords | HYDROLASE / SERINE PROTEASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Deepthi, S. / Johnson, A. / Pattabhi, V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structures of porcine beta-trypsin-detergent complexes: the stabilization of proteins through hydrophilic binding of polydocanol. Authors: Deepthi, S. / Johnson, A. / Pattabhi, V. #1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1999 Title: Crystal Structure at 1.63 Angstroms Resolution of the Native Form of Porcine Beta Trypsin : Revealing an Acetate Ion Binding Site and Functional Water Network Authors: Johnson, A. / Gautham, N. / Pattabhi, V. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: The First Structure at 1.8 Angstroms Resolution of an Active Autolysate Form of Porcine Alpha Trypsin Authors: Johnson, A. / Krishnaswamy, S. / Sundaram, P.V. / Pattabhi, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fni.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fni.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 1fni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/1fni ftp://data.pdbj.org/pub/pdb/validation_reports/fn/1fni | HTTPS FTP |
---|
-Related structure data
Related structure data | 1fmgC 1fn6C 1qquS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23491.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00761, trypsin | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | THE 223 AMINO ACIDS OF TRYPSIN ARE IDENTIFIED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.64 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.7 / Details: pH 6.70, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 6.7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 19, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→23.42 Å / Num. obs: 22228 / % possible obs: 82.68 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.0652 / Net I/σ(I): 20.08 |
Reflection shell | Resolution: 1.64→1.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4153 / Mean I/σ(I) obs: 1.76 / % possible all: 56.8 |
Reflection | *PLUS Num. measured all: 88932 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS Num. unique obs: 4475 / Rmerge(I) obs: 0.415 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QQU Resolution: 1.6→8 Å / Cross valid method: FREE R / σ(F): 0
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR,REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.64 Å / Rfactor all: 0.185 / Rfactor Rfree: 0.234 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|