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Open data
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Basic information
Entry | Database: PDB / ID: 3woi | ||||||
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Title | Crystal structure of the DAP BII (S657A) | ||||||
![]() | dipeptidyl aminopeptidase BII | ||||||
![]() | HYDROLASE / Chymotrypsin fold / S46 peptidase | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / proteolysis involved in protein catabolic process / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Nonaka, T. / Ogasawara, W. / Tanaka, N. | ||||||
![]() | ![]() Title: S46 peptidases are the first exopeptidases to be members of clan PA Authors: Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Masaki, M. / Ohta, K. / Okada, H. / Nonaka, T. / Morikawa, Y. / Nakamura, K.T. / ...Authors: Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Masaki, M. / Ohta, K. / Okada, H. / Nonaka, T. / Morikawa, Y. / Nakamura, K.T. / Ogasawara, W. / Tanaka, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298.4 KB | Display | ![]() |
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PDB format | ![]() | 248.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 472.8 KB | Display | |
Data in XML | ![]() | 60 KB | Display | |
Data in CIF | ![]() | 89.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wojC ![]() 3wokC ![]() 3wolC ![]() 3womC ![]() 3wonC ![]() 3wooC ![]() 3wopC ![]() 3woqC ![]() 3worC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 77075.727 Da / Num. of mol.: 2 / Mutation: S657A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: V5YM14, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 18% PEG8000, 20% Glycerol, 2mM ZnCl2, 80mM CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97897 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 90336 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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