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Yorodumi- PDB-2dew: Crystal structure of human peptidylarginine deiminase 4 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dew | ||||||
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Title | Crystal structure of human peptidylarginine deiminase 4 in complex with histone H3 N-terminal tail including Arg8 | ||||||
Components |
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Keywords | HYDROLASE / histone modification enzyme | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Arita, K. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Yamada, M. / Sato, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4 Authors: Arita, K. / Shimizu, T. / Hashimoto, H. / Hidaka, Y. / Yamada, M. / Sato, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dew.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dew.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 2dew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/2dew ftp://data.pdbj.org/pub/pdb/validation_reports/de/2dew | HTTPS FTP |
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-Related structure data
Related structure data | 2dexC 2deyC 1wdaS 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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Details | The second part of the biological assembly is generated by the two fold axis: -x, y, -z |
-Components
#1: Protein | Mass: 74933.836 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 / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UM07, protein-arginine deiminase | ||||
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#2: Protein/peptide | Mass: 1020.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | #5: 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: 2.9 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Imidazole (pH8.0), 0.2M lithium sulfate, 10% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2004 |
Radiation | Monochromator: bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.34 Å / Num. obs: 48003 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.1→2.17 Å / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WDA Resolution: 2.1→38.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.712 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.215 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.473 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.3945 Å / Origin y: 34.3901 Å / Origin z: 0.795 Å
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