[English] 日本語
![](img/lk-miru.gif)
- PDB-3gn0: Crystal structure of human arginase I in complex with difluoromet... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3gn0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human arginase I in complex with difluoromethylornithine (DFMO) | ||||||
![]() | Arginase-1 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / DFMO binding / polyamine biosynthesis / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Di Costanzo, L. / Christianson, D.W. | ||||||
![]() | ![]() Title: Binding of alpha,alpha-Disubstituted Amino Acids to Arginase Suggests New Avenues for Inhibitor Design Authors: Ilies, M. / Di Costanzo, L. / Dowling, D.P. / Thorn, K.J. / Christianson, D.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 138.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 108 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3gmzC ![]() 3sjtC ![]() 3skkC ![]() 3sl0C ![]() 3sl1C ![]() 2zavS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 14% JEFFAMINE 2001, 0.1M HEPES PH 7.0, 50MM BICINE PH 8.5, 1.4MM TYMINE, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.82 Å / Num. all: 67814 / Num. obs: 67814 / % possible obs: 99.9 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.412 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2ZAV Resolution: 1.7→33.82 Å / Cross valid method: THROUGHOUT Details: STRUCTURE IS AFFECTED BY PERFECT HEMIHEDRAL TWINNING. THE SUBMITTED INTENSITIES DATA ARE UNTWINNED, AND HAVE BEEN USED AS SUCH DURING THE REFINEMENT. THE TWINNING FACTOR IS -H,-K,L AND THE TWIN FRACTION IS = 0.5
| ||||||||||||||||||||
Displacement parameters | Biso mean: 25.003 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→33.82 Å
| ||||||||||||||||||||
Refine LS restraints |
|