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- PDB-6jtc: Crystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jtc | ||||||||||||||||||||||||||||||
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Title | Crystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 from Porphyromonas gingivalis (Space) | ||||||||||||||||||||||||||||||
![]() | Asp/Glu-specific dipeptidyl-peptidase | ||||||||||||||||||||||||||||||
![]() | HYDROLASE / dipeptidyl aminopeptidase / S46 / perio / Microgravity / antimicrobial | ||||||||||||||||||||||||||||||
Function / homology | ![]() developmental cell growth / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / peptide catabolic process / peptide binding / cell surface / proteolysis Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
![]() | Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Roppongi, S. / Kushibiki, C. / Nakamura, A. / Ogasawara, W. / Tanaka, N. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase. Authors: Sakamoto, Y. / Suzuki, Y. / Nakamura, A. / Watanabe, Y. / Sekiya, M. / Roppongi, S. / Kushibiki, C. / Iizuka, I. / Tani, O. / Sakashita, H. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / ...Authors: Sakamoto, Y. / Suzuki, Y. / Nakamura, A. / Watanabe, Y. / Sekiya, M. / Roppongi, S. / Kushibiki, C. / Iizuka, I. / Tani, O. / Sakashita, H. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / Honma, N. / Shida, Y. / Ogasawara, W. / Nakanishi-Matsui, M. / Nonaka, T. / Gouda, H. / 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 | ![]() | 289.7 KB | Display | ![]() |
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PDB format | ![]() | 233.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 50.5 KB | Display | |
Data in CIF | ![]() | 70.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jtbC ![]() 4y04S S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 82046.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561 Gene: dpp11, PGN_0607 / Production host: ![]() ![]() References: UniProt: B2RID1, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases #2: Chemical | ChemComp-GOL / | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.92 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 8.5 Details: 19 %(m/v) PEG 8000,0.18 M magnesium formate, 0.5 mM SH-5, 5 % (v/v) DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→116.94 Å / Num. obs: 70956 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 30.999 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.063 / Rrim(I) all: 0.169 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.39→2.43 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.283 / Num. unique obs: 3428 / CC1/2: 0.692 / Rpim(I) all: 0.502 / Rrim(I) all: 1.38 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Y04 Resolution: 2.39→39.65 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.199 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.637 Å2
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Refinement step | Cycle: 1 / Resolution: 2.39→39.65 Å
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Refine LS restraints |
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