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Open data
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Basic information
Entry | Database: PDB / ID: 7dke | ||||||||||||||||||||||||
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Title | Stenotrophomonas maltophilia DPP7 in complex with Phe-Tyr | ||||||||||||||||||||||||
![]() | Dipeptidyl-peptidase | ||||||||||||||||||||||||
![]() | HYDROLASE / dipeptidyl aminopeptidase / S46 / AMR / Microgravity / antimicrobial / chymotrypsin / serine protease | ||||||||||||||||||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / peptide catabolic process / proteolysis Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Sakamoto, Y. / Nakamura, A. / Suzuki, Y. / Honma, N. / Roppongi, S. / Kushibiki, C. / Yonezawa, N. / Takahashi, M. / Shida, Y. / Gouda, H. ...Sakamoto, Y. / Nakamura, A. / Suzuki, Y. / Honma, N. / Roppongi, S. / Kushibiki, C. / Yonezawa, N. / Takahashi, M. / Shida, Y. / Gouda, H. / Nonaka, T. / Ogasawara, W. / Tanaka, N. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7. Authors: Nakamura, A. / Suzuki, Y. / Sakamoto, Y. / Roppongi, S. / Kushibiki, C. / Yonezawa, N. / Takahashi, M. / Shida, Y. / Gouda, H. / Nonaka, T. / Tanaka, N. / Ogasawara, W. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305 KB | Display | ![]() |
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PDB format | ![]() | 235.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.1 KB | Display | ![]() |
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Full document | ![]() | 514.6 KB | Display | |
Data in XML | ![]() | 57.5 KB | Display | |
Data in CIF | ![]() | 84.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dkbSC ![]() 7dkcC ![]() 7dkdC 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 78061.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: R551-3 / Gene: Smal_0807 / Plasmid: pET22b / Production host: ![]() ![]() References: UniProt: B4SLK2, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M Ca Acetate, 20%w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→43.13 Å / Num. obs: 118877 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.163 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.064 / Rrim(I) all: 0.17 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.91→1.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 2 / Num. unique obs: 5580 / CC1/2: 0.631 / Rpim(I) all: 0.421 / % possible all: 93.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DKB Resolution: 1.91→40.003 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.97 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.157 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.301 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→40.003 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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