+Open data
-Basic information
Entry | Database: PDB / ID: 7dkb | ||||||||||||||||||||||||||||||
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Title | Stenotrophomonas maltophilia DPP7 in complex with Val-Tyr | ||||||||||||||||||||||||||||||
Components | Dipeptidyl-peptidase | ||||||||||||||||||||||||||||||
Keywords | HYDROLASE / dipeptidyl aminopeptidase / S46 / AMR / Microgravity / antimicrobial / chymotrypsin / serine protease | ||||||||||||||||||||||||||||||
Function / homology | Function and homology information 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 | Stenotrophomonas maltophilia (bacteria) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||||||||||||||||||||||||||
Authors | 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 | Japan, 9items
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Citation | Journal: Sci Rep / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dkb.cif.gz | 290.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dkb.ent.gz | 226 KB | Display | PDB format |
PDBx/mmJSON format | 7dkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/7dkb ftp://data.pdbj.org/pub/pdb/validation_reports/dk/7dkb | HTTPS FTP |
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-Related structure data
Related structure data | 7dkcC 7dkdC 7dkeC 3wolS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Stenotrophomonas maltophilia (strain R551-3) (bacteria) Strain: R551-3 / Gene: Smal_0807 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold(DE3) References: UniProt: B4SLK2, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M Amm Acetate, 20%w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→45.75 Å / Num. obs: 100498 / % possible obs: 93.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 18.556 Å2 / CC1/2: 0.397 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.1 / Rrim(I) all: 0.275 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.487 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3191 / CC1/2: 0.397 / Rpim(I) all: 0.576 / % possible all: 60.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WOL Resolution: 2.03→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.408 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.213 / ESU R Free: 0.182 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: 29.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→40 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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