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- PDB-4n2n: Crystal structure of Protein Arginine Deiminase 2 (E354A, 10 mM Ca2+) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4n2n | ||||||
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Title | Crystal structure of Protein Arginine Deiminase 2 (E354A, 10 mM Ca2+) | ||||||
![]() | Protein-arginine deiminase type-2 | ||||||
![]() | HYDROLASE / deiminase | ||||||
Function / homology | ![]() negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / protein-arginine deiminase activity / estrogen receptor signaling pathway / Chromatin modifying enzymes / transcription initiation-coupled chromatin remodeling / substantia nigra development ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase / protein-arginine deiminase activity / estrogen receptor signaling pathway / Chromatin modifying enzymes / transcription initiation-coupled chromatin remodeling / substantia nigra development / cellular response to leukemia inhibitory factor / nuclear estrogen receptor binding / euchromatin / azurophil granule lumen / chromatin remodeling / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Slade, D.J. / Zhang, X. / Fang, P. / Dreyton, C.J. / Zhang, Y. / Gross, M.L. / Guo, M. / Coonrod, S.A. / Thompson, P.R. | ||||||
![]() | ![]() Title: Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design. Authors: Slade, D.J. / Fang, P. / Dreyton, C.J. / Zhang, Y. / Fuhrmann, J. / Rempel, D. / Bax, B.D. / Coonrod, S.A. / Lewis, H.D. / Guo, M. / Gross, M.L. / Thompson, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.1 KB | Display | ![]() |
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PDB format | ![]() | 232.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.9 KB | Display | ![]() |
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Full document | ![]() | 456.8 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n20C ![]() 4n22C ![]() 4n24C ![]() 4n25SC ![]() 4n26C ![]() 4n28C ![]() 4n2aC ![]() 4n2bC ![]() 4n2cC ![]() 4n2dC ![]() 4n2eC ![]() 4n2fC ![]() 4n2gC ![]() 4n2hC ![]() 4n2iC ![]() 4n2kC ![]() 4n2lC ![]() 4n2mC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 78614.969 Da / Num. of mol.: 1 / Mutation: E354A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10-20% MPD, 50 mM MES, pH 5.6, 0.12 M sodium acetate, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2012 / Details: beryllium lenses |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→38.063 Å / Num. obs: 70612 / % possible obs: 99.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.081 |
Reflection shell | Highest resolution: 1.8 Å / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.3 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4N25 Resolution: 1.8→38.063 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8658 / SU ML: 0.5 / σ(F): 1.34 / Phase error: 20.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.662 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.99 Å2 / Biso mean: 29.3074 Å2 / Biso min: 9.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→38.063 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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