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Open data
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Basic information
Entry | Database: PDB / ID: 1qfm | ||||||
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Title | PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE | ||||||
![]() | PROTEIN (PROLYL OLIGOPEPTIDASE) | ||||||
![]() | HYDROLASE / PROLYL OLIGOPEPTIDASE / AMNESIA / ALPHA/BETA-HYDROLASE / BETA-PROPELLER | ||||||
Function / homology | ![]() prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fulop, V. | ||||||
![]() | ![]() Title: Prolyl oligopeptidase: an unusual beta-propeller domain regulates proteolysis. Authors: Fulop, V. / Bocskei, Z. / Polgar, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.1 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410 KB | Display | ![]() |
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Full document | ![]() | 412.2 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 80976.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: PORCINE BRAIN SEQUENCE WAS USED FOR STRUCTURE DETERMINATION AND REFINEMENT Source: (natural) ![]() ![]() | ||||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Nonpolymer details | 1-THIOXY-GLYCEROL (SGL781) IS COVALENTLY BOUND TO SER554 MONOTHIOGLYCEROL IS COVALENTLY BOUND TO ...1-THIOXY-GLYCEROL (SGL781) IS COVALENTLY | Sequence details | CYS25, CYS57 AND CYS255 ARE OXIDIZED WITH ONE OXYGEN ATOM. CYS175 AND CYS601 ARE OXIDIZED WITH TWO ...CYS25, CYS57 AND CYS255 ARE OXIDIZED WITH ONE OXYGEN ATOM. CYS175 AND CYS601 ARE OXIDIZED WITH TWO OXYGEN ATOMS. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: SEE REFERENCE, pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 140350 / % possible obs: 91 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.324 / % possible all: 80 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 30 Å / % possible obs: 91 % / Num. measured all: 366752 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 13.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |