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Yorodumi- PDB-1d3v: CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINA... -
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-Basic information
Entry | Database: PDB / ID: 1d3v | ||||||
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Title | CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG | ||||||
Components | PROTEIN (ARGINASE) | ||||||
Keywords | HYDROLASE / BINUCLEAR MANGANESE CLUSTER / BORONIC ACID INHIBITOR / PERFECTLY TWINNED CRYSTAL | ||||||
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 / Resolution: 1.7 Å | ||||||
Authors | Cox, J.D. / Kim, N.N. / Traish, A.M. / Christianson, D.W. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Arginase-boronic acid complex highlights a physiological role in erectile function. Authors: Cox, J.D. / Kim, N.N. / Traish, A.M. / 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 | 1d3v.cif.gz | 132.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d3v.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d3v ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d3v | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35019.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.1 / Details: pH 8.10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.927 |
Detector | Type: OTHER / Detector: CCD / Date: Aug 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.927 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 32367 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.125 / % possible all: 59.2 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. obs: 66822 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Num. measured all: 126870 |
-Processing
Software |
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Refinement | Resolution: 1.7→20 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.7→20 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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