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Yorodumi- PDB-2abr: Structure of D280A arginine deiminase with L-arginine forming a S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2abr | ||||||
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Title | Structure of D280A arginine deiminase with L-arginine forming a S-alkylthiouronium reaction intermediate | ||||||
Components | Arginine deiminase | ||||||
Keywords | HYDROLASE / arginine degradation pathway / L-arginine deiminase / catalytic mechanism | ||||||
Function / homology | Function and homology information arginine deiminase / arginine deiminase activity / arginine deiminase pathway / arginine catabolic process to ornithine / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.9 Å | ||||||
Authors | Galkin, A. / Lu, X. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal Structures Representing the Michaelis Complex and the Thiouronium Reaction Intermediate of Pseudomonas aeruginosa Arginine Deiminase. Authors: Galkin, A. / Lu, X. / Dunaway-Mariano, D. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2abr.cif.gz | 314.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2abr.ent.gz | 258.8 KB | Display | PDB format |
PDBx/mmJSON format | 2abr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/2abr ftp://data.pdbj.org/pub/pdb/validation_reports/ab/2abr | HTTPS FTP |
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-Related structure data
Related structure data | 2a9gC 2aafSC 2aciC 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 biological assembly is a tetramer generated from the molecules A, B, C and D in the asymmetric unit |
-Components
#1: Protein | Mass: 46605.059 Da / Num. of mol.: 4 / Mutation: D280A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: arcA / Plasmid: pET100/ADIn / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P13981, arginine deiminase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 38% MPD (2-methyl-2,4-pentanediol), 6% PEG 3350, 0.1 M Tris-HCl, L-arginine 0.02 M, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 23, 2003 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 36348 / Num. obs: 34967 / % possible obs: 96.2 % / Rmerge(I) obs: 0.103 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.263 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2AAF Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 45 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å
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