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Yorodumi- PDB-5olj: Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5olj | |||||||||||||||
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Title | Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 | |||||||||||||||
Components | Dipeptidyl peptidase IV | |||||||||||||||
Keywords | HYDROLASE / dipeptidyl peptidase 4 / peptidase inhibitor / Porphyromonas gingivalis / biofilm / dipeptidyl peptidase 9 | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Porphyromonas gingivalis (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||||||||
Authors | Fulop, V. | |||||||||||||||
Funding support | Belgium, 4items
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Citation | Journal: Eur J Med Chem / Year: 2017 Title: Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 and structure-activity relationships based on inhibitor profiling. Authors: Rea, D. / Van Elzen, R. / De Winter, H. / Van Goethem, S. / Landuyt, B. / Luyten, W. / Schoofs, L. / Van Der Veken, P. / Augustyns, K. / De Meester, I. / Fulop, V. / Lambeir, A.M. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2004 Title: Expression, purification and preliminary crystallographic analysis of dipeptidyl peptidase IV from Porphyromonas gingivalis. Authors: Rea, D. / Lambeir, A.M. / Kumagai, Y. / De Meester, I. / Scharpe, S. / Fulop, V. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5olj.cif.gz | 271.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5olj.ent.gz | 215.9 KB | Display | PDB format |
PDBx/mmJSON format | 5olj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5olj_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 5olj_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 5olj_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 5olj_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/5olj ftp://data.pdbj.org/pub/pdb/validation_reports/ol/5olj | HTTPS FTP |
-Related structure data
Related structure data | 5kbyS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 82087.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: dppIV, PGN_1469 / Production host: Porphyromonas gingivalis (bacteria) / References: UniProt: B2RKU3 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.02 M DLserine, and 0.1 M BICINE/TRIS pH 8.5 PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→38 Å / Num. obs: 48811 / % possible obs: 99.7 % / Redundancy: 9.3 % / Net I/σ(I): 10.8 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KBY Resolution: 2.2→37.87 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.81 / SU B: 9.784 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.204 / 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: 4.429 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→37.87 Å
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