+Open data
-Basic information
Entry | Database: PDB / ID: 4y06 | ||||||
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Title | Crystal structure of the DAP BII (G675R) dipeptide complex | ||||||
Components | Dipeptidyl aminopeptidase BII | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / proteolysis involved in protein catabolic process / protein homodimerization activity / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudoxanthomonas mexicana (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | ||||||
Authors | Sakamoto, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / 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 | 4y06.cif.gz | 293.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y06.ent.gz | 233.5 KB | Display | PDB format |
PDBx/mmJSON format | 4y06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/4y06 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y06 | HTTPS FTP |
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-Related structure data
Related structure data | 4xzyC 4y01C 4y02C 4y04C 3wolS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 78888.352 Da / Num. of mol.: 2 / Mutation: G675R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoxanthomonas mexicana (bacteria) / Gene: dapb2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: V5YM14 |
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-Non-polymers , 5 types, 547 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, glycerol, magnesium acetate, zinc chloride |
-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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 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: 2.18→36 Å / Num. obs: 88533 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rsym value: 0.08 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WOL Resolution: 2.18→36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.259 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.192 / 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: 41.074 Å2
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Refinement step | Cycle: 1 / Resolution: 2.18→36 Å
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Refine LS restraints |
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