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Yorodumi- PDB-3b1u: Crystal structure of human peptidylarginine deiminase 4 in comple... -
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-Basic information
Entry | Database: PDB / ID: 3b1u | ||||||
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Title | Crystal structure of human peptidylarginine deiminase 4 in complex with o-F-amidine | ||||||
Components | Protein-arginine deiminase type-4 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / nuclei / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Causey, C.P. / Jones, J.E. / Slack, J.L. / Kamei, D. / Jones Jr, L.E. / Subramanian, V. / Knuckley, B. / Ebrahimi, P. / Chumanevich, A.A. / Luo, Y. ...Causey, C.P. / Jones, J.E. / Slack, J.L. / Kamei, D. / Jones Jr, L.E. / Subramanian, V. / Knuckley, B. / Ebrahimi, P. / Chumanevich, A.A. / Luo, Y. / Hashimoto, H. / Shimizu, T. / Sato, M. / Hofseth, L.J. / Thompson, P.R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl- ...Title: The Development of N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-fluoro-1-iminoethyl)-l-ornithine Amide (o-F-amidine) and N-alpha-(2-Carboxyl)benzoyl-N(5)-(2-chloro-1-iminoethyl)-l-ornithine Amide (o-Cl-amidine) As Second Generation Protein Arginine Deiminase (PAD) Inhibitors Authors: Causey, C.P. / Jones, J.E. / Slack, J.L. / Kamei, D. / Jones Jr, L.E. / Subramanian, V. / Knuckley, B. / Ebrahimi, P. / Chumanevich, A.A. / Luo, Y. / Hashimoto, H. / Sato, M. / Hofseth, L.J. / 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 | 3b1u.cif.gz | 269.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b1u.ent.gz | 215.9 KB | Display | PDB format |
PDBx/mmJSON format | 3b1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/3b1u ftp://data.pdbj.org/pub/pdb/validation_reports/b1/3b1u | HTTPS FTP |
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-Related structure data
Related structure data | 3b1tC 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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-Components
#1: Protein | Mass: 74965.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PADI5, PDI5 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UM07, protein-arginine deiminase | ||||||
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#2: Chemical | ChemComp-YFF / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Sequence details | G55S, V82A AND G112A ARE NATURAL VARIANTS BASED ON REF 1 AND 4 OF DATABASE UNIPROT/SWISS-PROT ...G55S, V82A AND G112A ARE NATURAL VARIANTS BASED ON REF 1 AND 4 OF DATABASE UNIPROT/SWISS-PROT Q9UM07 (PADI4_HUMAN). | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 44771 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WDA Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 14.926 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R Free: 0.186 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.135 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -16.64 Å / Origin y: -0.0905 Å / Origin z: -1.4464 Å
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