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Yorodumi- PDB-4y04: Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y04 | ||||||
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Title | Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis (Space) | ||||||
Components | Peptidase S46 | ||||||
Keywords | HYDROLASE / Space / WT | ||||||
Function / homology | Function and homology information 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 | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. ...Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / Nonaka, T. / Ogasawara, W. / Tanaka, N. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2015 Title: Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity. Authors: Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / Gouda, H. / Nonaka, T. / Ogasawara, W. / Tanaka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y04.cif.gz | 169.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y04.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 4y04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y04_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 4y04_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 4y04_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 4y04_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/4y04 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y04 | HTTPS FTP |
-Related structure data
Related structure data | 4xzyC 4y01SC 4y02C 4y06C C: citing same article (ref.) S: Starting model for refinement |
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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: 82046.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: EG14_04230 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: A0A076NW73, UniProt: B2RID1*PLUS | ||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion Details: tri-potassium citrate, PEG 8000 Crystallisation under micro gravity at ISS Kibo. |
-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 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: 1.66→40 Å / Num. obs: 105914 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rsym value: 0.05 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.66→1.7 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.5 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y01 Resolution: 1.66→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.548 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / 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: 32.641 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→40 Å
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Refine LS restraints |
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