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Yorodumi- PDB-1rla: THREE-DIMENSIONAL STRUCTURE OF RAT LIVER ARGINASE, THE BINUCLEAR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rla | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF RAT LIVER ARGINASE, THE BINUCLEAR MANGANESE METALLOENZYME OF THE UREA CYCLE | ||||||
Components | ARGINASE | ||||||
Keywords | HYDROLASE / UREA CYCLE / ARGININE METABOLISM / MAGNESIUM | ||||||
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 / arginine metabolic process / negative regulation of T-helper 2 cell cytokine production / response to selenium ion / arginase / arginine catabolic process to ornithine ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / arginine metabolic process / negative regulation of T-helper 2 cell cytokine production / response to selenium ion / arginase / arginine catabolic process to ornithine / 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 / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / response to axon injury / response to vitamin E / response to amino acid / maternal process involved in female pregnancy / cellular response to interleukin-4 / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / cellular response to glucagon stimulus / 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 / adaptive immune response / response to lipopolysaccharide / 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 / Resolution: 2.1 Å | ||||||
Authors | Kanyo, Z. / Scolnick, L. / Ash, D. / Christianson, D.W. | ||||||
Citation | Journal: Nature / Year: 1996 Title: Structure of a unique binuclear manganese cluster in arginase. Authors: Kanyo, Z.F. / Scolnick, L.R. / Ash, D.E. / Christianson, D.W. #1: Journal: J.Mol.Biol. / Year: 1992 Title: Crystallization and Oligomeric Structure of Rat Liver Arginase Authors: Kanyo, Z.F. / Chen, C.Y. / Daghigh, F. / 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 | 1rla.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rla.ent.gz | 178.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rla_validation.pdf.gz | 380.3 KB | Display | wwPDB validaton report |
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Full document | 1rla_full_validation.pdf.gz | 394.1 KB | Display | |
Data in XML | 1rla_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1rla_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/1rla ftp://data.pdbj.org/pub/pdb/validation_reports/rl/1rla | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35019.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: PH 8.5 / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / References: UniProt: P07824, arginase #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop / Details: Kanyo, Z.F., (1992) J.Mol.Biol., 224, 1175. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Sep 17, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Rmerge(I) obs: 0.056 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 46162 / % possible obs: 91.6 % / Num. measured all: 147454 |
Reflection shell | *PLUS % possible obs: 58.3 % / Rmerge(I) obs: 0.365 |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.178 / Rfactor obs: 0.178 / σ(F): 2 | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | |||||||||||||||
Refinement | *PLUS Num. reflection obs: 47913 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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