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Open data
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Basic information
Entry | Database: PDB / ID: 4fci | ||||||
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Title | Crystal Structure of the Mn2+2-Human Arginase I-AGPA Complex | ||||||
![]() | Arginase-1 | ||||||
![]() | Hydrolase/Hydrolase inhibitor / Arginase Fold / Hydrolase / Hydrolase-Hydrolase inhibitor complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | D'Antonio, E.L. / Christianson, D.W. | ||||||
![]() | ![]() Title: Binding of the unreactive substrate analog L-2-amino-3-guanidinopropionic acid (dinor-L-arginine) to 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 | ![]() | 134.6 KB | Display | ![]() |
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PDB format | ![]() | 104.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 445.2 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fckC ![]() 2aebS C: citing same article ( S: Starting model for refinement |
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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 / Fragment: Human Arginase I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GPA / | #4: 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: 48.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: An unliganded Mn2+2-HAI crystal was soaked in 50 mM AGPA, 5 mM MnCl2, 100 mM bicine (pH 8.5), 32% (v/v) Jeffamine ED-2001 for 21 hours, 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: Nov 11, 2011 Details: Cryogenically cooled double crystal monochromater with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror. |
Radiation | Monochromator: Sagitally focused Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 18.056 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 9.313 / Rsym value: 0.183 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2AEB Resolution: 1.82→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: 25 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.82→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.89 Å
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