[English] 日本語
Yorodumi- PDB-1qfs: PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY BOUND I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qfs | ||||||
---|---|---|---|---|---|---|---|
Title | PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL | ||||||
Components | PROTEIN (PROLYL OLIGOPEPTIDASE) | ||||||
Keywords | HYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/BETA-HYDROLASE / BETA-PROPELLER | ||||||
Function / homology | Function and homology information prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å | ||||||
Authors | Fulop, V. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis. Authors: Fulop, V. / Bocskei, Z. / Polgar, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qfs.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qfs.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 1qfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qfs_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qfs_full_validation.pdf.gz | 460.2 KB | Display | |
Data in XML | 1qfs_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 1qfs_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qfs ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qfs | HTTPS FTP |
-Related structure data
Related structure data | 1qfmSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 80864.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: PORCINE BRAIN SEQUENCE WAS USED FOR STRUCTURE REFINEMENT Source: (natural) Sus scrofa (pig) / Cellular location: CYTOPLASM / Tissue: MUSCLE / References: UniProt: P23687, prolyl oligopeptidase |
---|---|
#2: Chemical | ChemComp-ZPR / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | Z-PRO-PROLINAL FORMS A HEMIACETAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 / Details: SEE REFERENCE, pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9096 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 51602 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.449 / % possible all: 92 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 135322 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER Starting model: 1QFM Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |