+Open data
-Basic information
Entry | Database: PDB / ID: 1hqx | ||||||
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Title | R308K ARGINASE VARIANT | ||||||
Components | ARGINASE | ||||||
Keywords | HYDROLASE / binuclear manganese cluster / mutagenesis / arginase / subunit-subunit interactions | ||||||
Function / homology | Function and homology information regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginine catabolic process to ornithine / response to selenium ion / arginase ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginine catabolic process to ornithine / response to selenium ion / arginase / arginase activity / urea cycle / response to methylmercury / response to vitamin A / response to herbicide / response to steroid hormone / response to manganese ion / Neutrophil degranulation / response to zinc ion / negative regulation of type II interferon-mediated signaling pathway / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / maternal process involved in female pregnancy / response to axon injury / response to vitamin E / response to amino acid / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / cellular response to interleukin-4 / positive regulation of endothelial cell proliferation / cellular response to dexamethasone stimulus / liver development / female pregnancy / lung development / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to lipopolysaccharide / adaptive immune response / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Lavulo, L.T. / Sossong Jr., T.M. / Brigham-Burke, M.R. / Doyle, M.L. / Cox, J.D. / Christianson, D.W. / Ash, D.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Subunit-subunit interactions in trimeric arginase. Generation of active monomers by mutation of a single amino acid. Authors: Lavulo, L.T. / Sossong Jr., T.M. / Brigham-Burke, M.R. / Doyle, M.L. / Cox, J.D. / Christianson, D.W. / Ash, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hqx.cif.gz | 181.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hqx.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hqx ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hqx | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 trimer |
-Components
#1: Protein | Mass: 34991.082 Da / Num. of mol.: 3 / Mutation: R308K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P07824, arginase #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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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: 2.38 Å3/Da / Density % sol: 48.28 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, BICINE, manganese chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: Kanyo, Z.F., (1992) J.Mol.Biol., 224, 1175. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.946445 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2000 |
Radiation | Monochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.946445 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 18649 / Num. obs: 18649 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.309 / % possible all: 81.3 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / % possible obs: 96 % / Num. measured all: 69842 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.263 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |