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- PDB-6jtb: Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jtb | ||||||||||||||||||||||||||||||
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Title | Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate 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 | ![]() | 176.2 KB | Display | ![]() |
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PDB format | ![]() | 134.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.6 KB | Display | ![]() |
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Full document | ![]() | 472.9 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jtcC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 82046.203 Da / Num. of mol.: 1 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 |
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-Non-polymers , 5 types, 835 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.8 % |
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Crystal grow | Temperature: 293 K / Method: counter-diffusion / pH: 8.5 Details: 20 % (m/v) PEG 8000, 0.2 M tri-potassium citrate, microgravity environment in the Kibo, ISS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→49.56 Å / Num. obs: 144097 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 18.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7050 / CC1/2: 0.688 / Rpim(I) all: 0.352 / Rrim(I) all: 0.764 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Y04 Resolution: 1.5→49.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.197 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / 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: 23.543 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→49.56 Å
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Refine LS restraints |
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