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Yorodumi- PDB-3skk: Crystal structure of human arginase I in complex with the inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3skk | ||||||
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Title | Crystal structure of human arginase I in complex with the inhibitor FABH, Resolution 1.70 A, twinned structure | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ABH inhibitor derivative / twinning / 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 / negative regulation of type II interferon-mediated signaling pathway / urea cycle / 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 / negative regulation of type II interferon-mediated signaling pathway / urea cycle / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å | ||||||
Authors | Thorn, K.J. / Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3skk.cif.gz | 149.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3skk.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 3skk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3skk_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 3skk_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 3skk_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 3skk_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/3skk ftp://data.pdbj.org/pub/pdb/validation_reports/sk/3skk | HTTPS FTP |
-Related structure data
Related structure data | 3gmzC 3gn0C 3sjtC 3sl0C 3sl1C 2zavS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: 34779.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pet11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE STARTING MATERIAL 2-AMINO-6-BORONO-2-(DIFLUOROMETHYL)HEXANOIC ACID (FABH) UNDERGOES TO ...THE STARTING MATERIAL 2-AMINO-6-BORONO-2-(DIFLUOROME | |
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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: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 3 uL of protein solution [3.5 mg/mL HAI, 50 mM bicine (pH 8.5), 2 mM FABH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 22-28% Jeffamine] were equilibrated against a ...Details: 3 uL of protein solution [3.5 mg/mL HAI, 50 mM bicine (pH 8.5), 2 mM FABH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 22-28% Jeffamine] were equilibrated against a 1 mL reservoir of precipitant solution, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.5 |
Reflection | Resolution: 1.7→50 Å / Num. all: 66860 / Num. obs: 66860 / % possible obs: 99 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.3 / % possible all: 98.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZAV Resolution: 1.701→37.779 Å / σ(F): 0.13 / Phase error: 24.55 / 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 / Bsol: 43.417 Å2 / ksol: 0.324 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.701→37.779 Å
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Refine LS restraints |
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LS refinement shell |
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