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Yorodumi- PDB-5yp4: Crystal structure of dipeptidyl peptidase IV (DPP IV) with Lys-Pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yp4 | |||||||||||||||||||||||||||||||||
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Title | Crystal structure of dipeptidyl peptidase IV (DPP IV) with Lys-Pro from Pseudoxanthomonas mexicana WO24 | |||||||||||||||||||||||||||||||||
Components | Dipeptidyl aminopeptidase 4 | |||||||||||||||||||||||||||||||||
Keywords | HYDROLASE / DAP IV / Clan SC S9 / peptidase / DPP4 / DPP8 / DPP9 | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / aminopeptidase activity / serine-type peptidase activity / proteolysis involved in protein catabolic process / periplasmic space / protein homodimerization activity / identical protein binding / cytoplasm Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Pseudoxanthomonas mexicana (bacteria) | |||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||||||||||||||||||||||||||
Authors | Roppongi, S. / Suzuki, Y. / Tateoka, C. / Fuimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. ...Roppongi, S. / Suzuki, Y. / Tateoka, C. / Fuimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. / Tanaka, N. / Sakamoto, Y. / Nonaka, T. | |||||||||||||||||||||||||||||||||
Funding support | Japan, 10items
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Citation | Journal: Sci Rep / Year: 2018 Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues. Authors: Roppongi, S. / Suzuki, Y. / Tateoka, C. / Fujimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. / Tanaka, N. / Sakamoto, Y. / Nonaka, T. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yp4.cif.gz | 616.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yp4.ent.gz | 503.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yp4_validation.pdf.gz | 511.1 KB | Display | wwPDB validaton report |
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Full document | 5yp4_full_validation.pdf.gz | 544.2 KB | Display | |
Data in XML | 5yp4_validation.xml.gz | 127 KB | Display | |
Data in CIF | 5yp4_validation.cif.gz | 190.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/5yp4 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/5yp4 | HTTPS FTP |
-Related structure data
Related structure data | 5yp1SC 5yp2C 5yp3C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 82375.500 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoxanthomonas mexicana (bacteria) / Strain: WO24 / Gene: dap4 / Plasmid: pUC19 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q6F3I7, dipeptidyl-peptidase IV #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-LYS / #4: Chemical | ChemComp-PRO / #5: Water | ChemComp-HOH / | Sequence details | Residue M12I is mutagenesis according to sequence database UniportKB Q6F3I7 (DAP4_PSEMX). | |
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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: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 20000, 80mM MES pH6.5, 20% Glycerol, 4mM Lys-Pro |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 245086 / % possible obs: 94.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.073 / Rrim(I) all: 0.11 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2 / Num. unique obs: 27199 / Rpim(I) all: 0.282 / Rrim(I) all: 0.425 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YP1 Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.336 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.731 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→40 Å
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Refine LS restraints |
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