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- PDB-6q92: Crystal structure of human Arginase-1 at pH 7.0 in complex with ABH -
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Open data
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Basic information
Entry | Database: PDB / ID: 6q92 | ||||||
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Title | Crystal structure of human Arginase-1 at pH 7.0 in complex with ABH | ||||||
![]() | Arginase-1 | ||||||
![]() | HYDROLASE / hydrolase inhibitor / borate / manganese cluster / pH-dependent | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Grobben, Y. / Uitdehaag, J.C.M. / Zaman, G.J.R. | ||||||
![]() | ![]() Title: Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158. Authors: Grobben, Y. / Uitdehaag, J.C.M. / Willemsen-Seegers, N. / Tabak, W.W.A. / de Man, J. / Buijsman, R.C. / Zaman, G.J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.9 KB | Display | ![]() |
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PDB format | ![]() | 114.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4 MB | Display | ![]() |
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Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 45.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6q9pC ![]() 6qafC ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 36951.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal his tag with thrombin cleavage site / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % / Description: clear rod-like hexagonal crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Crystals were generated from 22 % PEG 1500, 0.2 M MIB buffer pH 4.0 (sodium malonate, imidazole and boric acid in a 2:3:3 molar ratio). Crystals were equilibrated to soaking solution (22 % ...Details: Crystals were generated from 22 % PEG 1500, 0.2 M MIB buffer pH 4.0 (sodium malonate, imidazole and boric acid in a 2:3:3 molar ratio). Crystals were equilibrated to soaking solution (22 % PEG 1500, 0.2 M MMT buffer pH 7.0 (DL-malic acid, MES, Tris base in a 1:2:2 molar ratio). Subsequently, crystals were gradually soaked for 13 days in soaking solution containing 15 mM ABH. Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 6, 2017 / Details: transfocator | |||||||||||||||
Radiation | Monochromator: diamond beam splitter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.5→39.14 Å / Num. obs: 99464 / % possible obs: 98.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 13.91 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.074 / Rrim(I) all: 0.122 / Χ2: 0.93 / Net I/σ(I): 6.9 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4790 / CC1/2: 0.293 / Rpim(I) all: 0.508 / Rrim(I) all: 0.796 / Χ2: 0.82 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2AEB Resolution: 1.5→39.14 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.679 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.011 Details: Hydrogens have been added in riding positions. Refinement with 'crystal is twinned' switched on. Refinement of anisotropic B-factors for the Manganese cluster only.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.294 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→39.14 Å
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Refine LS restraints |
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