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- PDB-3kv2: HIGH RESOLUTION STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH THE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kv2 | ||||||
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Title | HIGH RESOLUTION STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH THE STRONG INHIBITOR N(omega)-hydroxy-nor-L-arginine (nor-NOHA) | ||||||
![]() | Arginase-1 | ||||||
![]() | HYDROLASE / STRONG INHIBITOR / nor-NOHA / ARGINASE / HIGH RESOLUTION / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Polymorphism / Urea cycle | ||||||
Function / homology | ![]() positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Di Costanzo, L. / Christianson, D.W. | ||||||
![]() | ![]() Title: Inhibition of human arginase I by substrate and product analogues. Authors: Di Costanzo, L. / Ilies, M. / Thorn, K.J. / Christianson, D.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.6 KB | Display | ![]() |
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PDB format | ![]() | 105.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455 KB | Display | ![]() |
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Full document | ![]() | 466 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 38.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lp4C ![]() 3lp7C ![]() 2zavS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34779.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: Hanging drops containing 3 L protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM nor-NOHA, 100 M MnCl2] and 3 L precipitant solution [0.1 M bis-Tris (pH 6.5), 28% PEG monomethyl ...Details: Hanging drops containing 3 L protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM nor-NOHA, 100 M MnCl2] and 3 L precipitant solution [0.1 M bis-Tris (pH 6.5), 28% PEG monomethyl ether 2000] were equilibrated over a 1 mL reservoir of precipitant solution at 2 C. , VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 90987 / Num. obs: 90987 / % possible obs: 98.2 % / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 2 % / Rmerge(I) obs: 0.302 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: PHASER Starting model: 2ZAV monomer A Resolution: 1.55→50 Å Details: Data in the structure factor file is twinned. The operator is -h,-k,l, and the fraction is 0.5
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Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.61 Å /
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