+Open data
-Basic information
Entry | Database: PDB / ID: 4ity | ||||||
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Title | Crystal structure of Leishmania mexicana arginase | ||||||
Components | Arginase | ||||||
Keywords | HYDROLASE / arginase fold | ||||||
Function / homology | Function and homology information arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / manganese ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 4ity.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ity.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ity.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ity_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 4ity_full_validation.pdf.gz | 444.9 KB | Display | |
Data in XML | 4ity_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4ity_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/4ity ftp://data.pdbj.org/pub/pdb/validation_reports/it/4ity | HTTPS FTP |
-Related structure data
Related structure data | 4iu0SC 4iu1C 4iu4C 4iu5C 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 | ChemComp-GOL / | ||
#3: Chemical | #4: 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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 1.4 mM thymine, 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 3 uL precipitant solution (10% w/v PEG10000, ...Details: 3 uL protein solution (7.0 mg/mL delta-12-LmARG, 45 mM bicine, pH 8.5, 1.4 mM thymine, 90 uM manganese chloride, 4.5% v/v glycerol, 1.8 mM BME) + 3 uL precipitant solution (10% w/v PEG10000, 5% v/v MPD, 0.1 M HEPES, pH 7.3) equilibrated against 500 uL precipitant solution on a siliconized cover slide, 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: 0.37 |
Reflection | Resolution: 1.8→50 Å / Num. all: 31867 / Num. obs: 31710 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 16.91 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.775 / Rsym value: 0.525 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4IU0 Resolution: 1.8→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 76.6096 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å /
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Xplor file |
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