+Open data
-Basic information
Entry | Database: PDB / ID: 1pq5 | ||||||
---|---|---|---|---|---|---|---|
Title | Trypsin at pH 5, 0.85 A | ||||||
Components | Trypsin | ||||||
Keywords | HYDROLASE / trypsin / serine protease / catalysis | ||||||
Function / homology | Function and homology information trypsin / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.85 Å | ||||||
Authors | Schmidt, A. / Jelsch, C. / Rypniewski, W. / Lamzin, V.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Trypsin Revisited: CRYSTALLOGRAPHY AT (SUB) ATOMIC RESOLUTION AND QUANTUM CHEMISTRY REVEALING DETAILS OF CATALYSIS. Authors: Schmidt, A. / Jelsch, C. / Ostergaard, P. / Rypniewski, W. / Lamzin, V.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pq5.cif.gz | 150.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pq5.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pq5 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pq5 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22200.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P35049, trypsin | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-ARG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.52 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Na sulphate, Na citrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Rypniewski, W.R., (1993) Protein Eng., 6, 341. / PH range low: 5.5 / PH range high: 5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.811 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 20, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 0.83→35 Å / Num. all: 146915 / Num. obs: 146915 / % possible obs: 91.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 4.99 Å2 / Rsym value: 0.033 / Net I/σ(I): 34 |
Reflection shell | Resolution: 0.83→0.84 Å / Redundancy: 2 % / Mean I/σ(I) obs: 7.22 / Num. unique all: 3215 / Rsym value: 0.101 / % possible all: 80.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 146839 / Rmerge(I) obs: 0.033 |
Reflection shell | *PLUS Mean I/σ(I) obs: 7.2 |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 0.85→30 Å / Num. parameters: 20006 / Num. restraintsaints: 25358 / Stereochemistry target values: ENGH AND HUBER Details: initially Rfree (building stage) was used (10% of data at random), later Rfree was not used.
| ||||||||||||||||
Refine analyze | Num. disordered residues: 43 / Occupancy sum hydrogen: 1500.73 / Occupancy sum non hydrogen: 1998.19 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.85→30 Å
| ||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 96 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 0.83 Å / Rfactor Rwork: 0.098 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |