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Yorodumi- PDB-4x8c: Crystal structure of human peptidylarginine deiminase type4 (PAD4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x8c | ||||||
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Title | Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with GSK147 | ||||||
Components | Protein-arginine deiminase type-4 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å | ||||||
Authors | Lewis, H.D. / Bax, B.D. / Chung, C.-W. / Polyakova, O. / Thorpe, J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2015 Title: Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation. Authors: Lewis, H.D. / Liddle, J. / Coote, J.E. / Atkinson, S.J. / Barker, M.D. / Bax, B.D. / Bicker, K.L. / Bingham, R.P. / Campbell, M. / Chen, Y.H. / Chung, C.W. / Craggs, P.D. / Davis, R.P. / ...Authors: Lewis, H.D. / Liddle, J. / Coote, J.E. / Atkinson, S.J. / Barker, M.D. / Bax, B.D. / Bicker, K.L. / Bingham, R.P. / Campbell, M. / Chen, Y.H. / Chung, C.W. / Craggs, P.D. / Davis, R.P. / Eberhard, D. / Joberty, G. / Lind, K.E. / Locke, K. / Maller, C. / Martinod, K. / Patten, C. / Polyakova, O. / Rise, C.E. / Rudiger, M. / Sheppard, R.J. / Slade, D.J. / Thomas, P. / Thorpe, J. / Yao, G. / Drewes, G. / Wagner, D.D. / Thompson, P.R. / Prinjha, R.K. / Wilson, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x8c.cif.gz | 228.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x8c.ent.gz | 180.7 KB | Display | PDB format |
PDBx/mmJSON format | 4x8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/4x8c ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x8c | HTTPS FTP |
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-Related structure data
Related structure data | 4x8gC 3apnS 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: 74917.836 Da / Num. of mol.: 1 / Mutation: C645A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PADI5, PDI5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9UM07, protein-arginine deiminase | ||||
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#2: Chemical | #3: Chemical | ChemComp-3YZ / [( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.8 Details: 100 mM imidazole, pH 7.8, 200 mM Li2SO4, 2 mM TCEP, 6-7.5% PEG 2K MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→19.84 Å / Num. obs: 14431 / % possible obs: 95 % / Redundancy: 2.9 % / Net I/σ(I): 10.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3APN Resolution: 3.1→19.836 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.78 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→19.836 Å
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Refine LS restraints |
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LS refinement shell |
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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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