+Open data
-Basic information
Entry | Database: PDB / ID: 4hww | ||||||
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Title | Crystal structure of human Arginase-1 complexed with inhibitor 9 | ||||||
Components | Arginase-1 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / metalloenzyme / alpha/beta fold / Hydrolase / Arginine metabolism / Manganese / Hydrolase-Hydrolase Inhibitor complex | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.298 Å | ||||||
Authors | Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Whitehouse, D.L. / Golebiowski, A. / Ji, M. / Zhang, M. / Beckett, P. / Sheeler, R. / Andreoli, M. ...Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Whitehouse, D.L. / Golebiowski, A. / Ji, M. / Zhang, M. / Beckett, P. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / Schroeter, H. / Van Zandt, M.C. / Podjarny, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Discovery of (R)-2-Amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic Acid and Congeners As Highly Potent Inhibitors of Human Arginases I and II for Treatment of Myocardial Reperfusion Injury. Authors: Van Zandt, M.C. / Whitehouse, D.L. / Golebiowski, A. / Ji, M.K. / Zhang, M. / Beckett, R.P. / Jagdmann, G.E. / Ryder, T.R. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / ...Authors: Van Zandt, M.C. / Whitehouse, D.L. / Golebiowski, A. / Ji, M.K. / Zhang, M. / Beckett, R.P. / Jagdmann, G.E. / Ryder, T.R. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / D'Angelo, G. / Mitschler, A. / Cousido-Siah, A. / Ruiz, F.X. / Howard, E.I. / Podjarny, A.D. / Schroeter, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hww.cif.gz | 144.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hww.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hww_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4hww_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4hww_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 4hww_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/4hww ftp://data.pdbj.org/pub/pdb/validation_reports/hw/4hww | HTTPS FTP |
-Related structure data
Related structure data | 4hxqC 4hzeC 4i06C 1d3vS 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 on special symmetry positions |
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Details | biological assembly is a trimer generated from monomer A in the asymmetric unit by the operations: -x+y, -x, z-l; -y, x-y, z+1; or from monomer B in the asymmetric unit by the operations: -x+y, -x, z; -y, x-y, z |
-Components
#1: Protein | Mass: 33923.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05089, arginase #2: Chemical | #3: Chemical | ChemComp-MN / #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: 2.4 Å3/Da / Density % sol: 48.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM Malonic Acid, Imidazol, Boric system, 25% Polyethylene Glycol (PEG) 1500, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91907 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91907 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: -h,-k,l / Fraction: 0.48 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.298→50 Å / Num. all: 155548 / Num. obs: 155548 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.051 / Χ2: 1.026 / Net I/σ(I): 12.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1D3V Resolution: 1.298→25.919 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8992 / Cross valid method: R-free / σ(F): 0 / Phase error: 17.44 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 24.89 Å2 / Biso mean: 10.7663 Å2 / Biso min: 5.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.298→25.919 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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