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Yorodumi- PDB-3kv2: HIGH RESOLUTION STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH THE... -
+Open data
-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) | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / STRONG INHIBITOR / nor-NOHA / ARGINASE / HIGH RESOLUTION / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Polymorphism / Urea cycle | ||||||
Function / homology | Function and homology information positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginine catabolic process to ornithine / arginase / arginase activity / 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 / arginine catabolic process to ornithine / arginase / arginase activity / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.55 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kv2.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kv2.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kv/3kv2 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/3kv2 | HTTPS FTP |
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-Related structure data
Related structure data | 3lp4C 3lp7C 2zavS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: ARG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, 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: 2.37 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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å |
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 |
-Processing
Software |
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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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