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Yorodumi- PDB-4n2c: Crystal structure of Protein Arginine Deiminase 2 (F221/222A, 10 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n2c | ||||||
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Title | Crystal structure of Protein Arginine Deiminase 2 (F221/222A, 10 mM Ca2+) | ||||||
Components | Protein-arginine deiminase type-2 | ||||||
Keywords | HYDROLASE / deiminase | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.022 Å | ||||||
Authors | Slade, D.J. / Zhang, X. / Fang, P. / Dreyton, C.J. / Zhang, Y. / Gross, M.L. / Guo, M. / Coonrod, S.A. / Thompson, P.R. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n2c.cif.gz | 266.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n2c.ent.gz | 212 KB | Display | PDB format |
PDBx/mmJSON format | 4n2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n2c_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 4n2c_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | 4n2c_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 4n2c_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/4n2c ftp://data.pdbj.org/pub/pdb/validation_reports/n2/4n2c | HTTPS FTP |
-Related structure data
Related structure data | 4n20C 4n22C 4n24C 4n25SC 4n26C 4n28C 4n2aC 4n2bC 4n2dC 4n2eC 4n2fC 4n2gC 4n2hC 4n2iC 4n2kC 4n2lC 4n2mC 4n2nC 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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Unit cell |
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-Components
#1: Protein | Mass: 78520.812 Da / Num. of mol.: 1 / Mutation: F221A,F222A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PADI2, KIAA0994, PDI2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J8, protein-arginine deiminase | ||
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#2: Chemical | ChemComp-CA / #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: 2.47 Å3/Da / Density % sol: 50.13 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10% MPD, 10% ethanol, 50 mM MES, pH 5.6, 20 mM magnesium chloride, 1 mM spermidine, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.2836 Å |
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2012 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2836 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→48.955 Å / Num. obs: 13566 / % possible obs: 98.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.33 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 17 |
Reflection shell | Highest resolution: 3.02 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4N25 Resolution: 3.022→48.955 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8073 / SU ML: 0.63 / σ(F): 1.36 / Phase error: 26.08 / 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: 5.711 Å2 / ksol: 0.292 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.32 Å2 / Biso mean: 36.3383 Å2 / Biso min: 11.24 Å2
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Refinement step | Cycle: LAST / Resolution: 3.022→48.955 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: 5
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Refinement TLS params. | Method: refined / Origin x: 203.5296 Å / Origin y: -0.3744 Å / Origin z: 15.4932 Å
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Refinement TLS group | Selection details: all |