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Yorodumi- PDB-6i0x: Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i0x | ||||||
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Title | Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant G231N/E232T/N235D in complex with Cl-amidine. | ||||||
Components | Peptidylarginine deiminaseProtein-arginine deiminase | ||||||
Keywords | HYDROLASE / citrullination / odontopathogenic virulence factor / arginine demininase / periodontal disease / rheumatoid arthitis | ||||||
Function / homology | Function and homology information Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines / putrescine biosynthetic process / protein-arginine deiminase activity / extracellular region Similarity search - Function | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Gomis-Ruth, F.X. / Goulas, T. / Sola, M. / Potempa, J. | ||||||
Citation | Journal: Protein Sci. / Year: 2019 Title: Structure, function, and inhibition of a genomic/clinical variant of Porphyromonas gingivalis peptidylarginine deiminase. Authors: Bereta, G. / Goulas, T. / Madej, M. / Bielecka, E. / Sola, M. / Potempa, J. / Xavier Gomis-Ruth, F. #1: Journal: Sci Rep / Year: 2015 Title: Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase. Authors: Goulas, T. / Mizgalska, D. / Garcia-Ferrer, I. / Kantyka, T. / Guevara, T. / Szmigielski, B. / Sroka, A. / Millan, C. / Uson, I. / Veillard, F. / Potempa, B. / Mydel, P. / Sola, M. / ...Authors: Goulas, T. / Mizgalska, D. / Garcia-Ferrer, I. / Kantyka, T. / Guevara, T. / Szmigielski, B. / Sroka, A. / Millan, C. / Uson, I. / Veillard, F. / Potempa, B. / Mydel, P. / Sola, M. / Potempa, J. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i0x.cif.gz | 366.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i0x.ent.gz | 294.8 KB | Display | PDB format |
PDBx/mmJSON format | 6i0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i0x ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i0x | HTTPS FTP |
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-Related structure data
Related structure data | 4ytbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49095.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The present is a triple point mutant G231N/E232T/N235D. In addition, catalytic cysteine C351 is covalently modified by the inhibitor Cl-amidine resulting in new residue CYA. Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria) Strain: ATCC BAA-308 / W83 / Gene: PG_1424 / Production host: Porphyromonas gingivalis (bacteria) References: UniProt: Q9RQJ2, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium acetate, 15% [w/v] polyethylene glycol 3,350, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979294 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979294 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→62.1 Å / Num. obs: 119834 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.6→1.7 Å / Rmerge(I) obs: 0.562 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YTB Resolution: 1.6→62.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.079
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Displacement parameters | Biso mean: 24.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→62.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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