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Yorodumi- PDB-1hqf: CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINA... -
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-Basic information
Entry | Database: PDB / ID: 1hqf | ||||||
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Title | CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH N-HYDROXY-L-ARGININE | ||||||
Components | ARGINASE 1Arginase | ||||||
Keywords | HYDROLASE / arginase / N-Hydroxy-L-Arginine (NOHA) / binuclear manganese cluster / metalloenzyme | ||||||
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 / negative regulation of T cell proliferation / response to axon injury / response to vitamin E / response to amino acid / response to cadmium ion / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / cellular response to interleukin-4 / 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: 2.9 Å | ||||||
Authors | Cox, J.D. / Cama, E. / Colleluori, D.M. / Ash, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Mechanistic and metabolic inferences from the binding of substrate analogues and products to arginase. Authors: Cox, J.D. / Cama, E. / Colleluori, D.M. / Pethe, S. / Boucher, J.L. / Mansuy, D. / Ash, D.E. / 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 | 1hqf.cif.gz | 187.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hqf.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 1hqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hqf ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hqf | HTTPS FTP |
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-Related 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: 35019.098 Da / Num. of mol.: 3 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: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 | *PLUS Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2000 |
Radiation | Monochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 17524 / Num. obs: 17424 / % possible obs: 83.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.302 / % possible all: 86.7 |
Reflection | *PLUS Num. obs: 17524 / Num. measured all: 31263 |
Reflection shell | *PLUS % possible obs: 96.7 % / Num. unique obs: 781 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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