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- PDB-4ytg: Crystal structure of Porphyromonas gingivalis peptidylarginine de... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ytg | ||||||
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Title | Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant C351A in complex with dipeptide Met-Arg. | ||||||
![]() | Peptidylarginine deiminase | ||||||
![]() | HYDROLASE / Peptidylarginine deiminase / citrullination | ||||||
Function / homology | ![]() Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines / agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Goulas, T. / Mizgalska, D. / Garcia-Ferrer, I. / Kantyka, T. / Guevara, T. / Szmigielski, B. / Sroka, A. / Millan, C. / Uson, I. / Veillard, F. ...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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.5 KB | Display | ![]() |
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PDB format | ![]() | 150.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4yt9SC ![]() 4ytbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48204.707 Da / Num. of mol.: 1 / Fragment: residues 44-475 / Mutation: C351A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: PG_1424 / Production host: ![]() References: UniProt: Q9RQJ2, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines |
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-Non-polymers , 8 types, 438 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CYS.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-CYS / | ||||||
#4: Chemical | ChemComp-MET / | ||||||
#5: Chemical | ChemComp-ARG / | ||||||
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM tri-sodium citrate, 20% [w/v] polyethylene glycol 3,000, pH5.5-6.5 PH range: 5.5-6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→67.9 Å / Num. obs: 38882 / % possible obs: 99.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5771 / CC1/2: 0.927 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4yt9 Resolution: 1.8→48.57 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9473 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.102
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Displacement parameters | Biso mean: 28.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.192 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→48.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 19
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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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