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Open data
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Basic information
Entry | Database: PDB / ID: 3tf3 | ||||||
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Title | Crystal structure of metal-free Human Arginase I | ||||||
![]() | Arginase-1 | ||||||
![]() | HYDROLASE / ARGINASE FOLD | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | D'Antonio, E.L. / Christianson, D.W. | ||||||
![]() | ![]() Title: Crystal structures of complexes with cobalt-reconstituted human arginase I. Authors: D'Antonio, E.L. / 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 | ![]() | 130.9 KB | Display | ![]() |
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PDB format | ![]() | 102.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3th7C ![]() 3theC ![]() 3thhC ![]() 3thjC ![]() 2aebS 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES, 30% (v/v) Jeffamine ED-2001, 0.014 M thymine, 0.0001 M manganese chloride. following xtal growth, metal-free HAI crystals are prepared by soaking a single crystal in 0.015 M ...Details: 0.1 M HEPES, 30% (v/v) Jeffamine ED-2001, 0.014 M thymine, 0.0001 M manganese chloride. following xtal growth, metal-free HAI crystals are prepared by soaking a single crystal in 0.015 M dipicolinic acid, 0.015 M EDTA, 30% (v/v) Jeffamine ED-2001 for 1 week, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2010 Details: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 77810 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 35.185 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.459 / Rsym value: 0.43 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AEB Resolution: 1.64→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.64→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.7 Å
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