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Yorodumi- PDB-4iu5: Crystal structure of Leishmania mexicana arginase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iu5 | ||||||
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Title | Crystal structure of Leishmania mexicana arginase in complex with catalytic product L-ornithine | ||||||
Components | Arginase | ||||||
Keywords | HYDROLASE / arginase fold | ||||||
Function / homology | Function and homology information arginine metabolic process / arginase / arginase activity / urea cycle / metal ion binding Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | D'Antonio, E.L. / Ullman, B. / Roberts, S.C. / Gaur Dixit, U. / Wilson, M.E. / Hai, Y. / Christianson, D.W. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2013 Title: Crystal structure of arginase from Leishmania mexicana and implications for the inhibition of polyamine biosynthesis in parasitic infections. Authors: D'Antonio, E.L. / Ullman, B. / Roberts, S.C. / Dixit, U.G. / Wilson, M.E. / Hai, Y. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iu5.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iu5.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 4iu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4iu5 ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iu5 | HTTPS FTP |
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-Related structure data
Related structure data | 4itySC 4iu0C 4iu1C 4iu4C S: Starting model for refinement C: citing same article (ref.) |
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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: 36034.449 Da / Num. of mol.: 1 / Fragment: UNP residues 13-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Gene: ARG / Plasmid: pET200/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6TUJ5, arginase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ORN / | #4: Chemical | ChemComp-GOL / | #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: 2.45 Å3/Da / Density % sol: 49.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 10 mM DL-alpha-difluoromethylornithine (DFMO), 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 3 uL ...Details: 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 10 mM DL-alpha-difluoromethylornithine (DFMO), 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 3 uL precipitant solution (0.1 M HEPES, pH 7.5, 12% w/v PEG3350) equilibrated against 500 uL precipitant solution on a siliconized cover slide, crystals grow within one week, soaked in 10 uL 50 mM L-ornithine, 0.1 M HEPPS, pH 8.5, 15% w/v PEG3350 for 23 hours, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2012 |
Radiation | Monochromator: Cryogenically cooled double-crystal Si(111) with horizontally focusing, sagitally bent second crystal with 4:1 magnification ratio and vertically focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.3 |
Reflection | Resolution: 1.95→50 Å / Num. all: 24954 / Num. obs: 24877 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 20.195 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.711 / Rsym value: 0.624 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4ITY Resolution: 1.95→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 58.5924 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å /
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Xplor file |
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