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Yorodumi- PDB-3e6k: X-ray structure of Human Arginase I: the mutant D183A in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e6k | ||||||
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Title | X-ray structure of Human Arginase I: the mutant D183A in complex with ABH | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / mutant D183 / amino acid recognition / ABH / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Polymorphism / Urea cycle | ||||||
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: 2.1 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Probing the specificity determinants of amino acid recognition by arginase. Authors: Shishova, E.Y. / Di Costanzo, L. / Emig, F.A. / Ash, D.E. / 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 | 3e6k.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e6k.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e6k_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 3e6k_full_validation.pdf.gz | 482.9 KB | Display | |
Data in XML | 3e6k_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 3e6k_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/3e6k ftp://data.pdbj.org/pub/pdb/validation_reports/e6/3e6k | HTTPS FTP |
-Related structure data
Related structure data | 3e6vC 3e8qC 3e8zC 3e9bC 2aebS 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
#1: Protein | Mass: 34735.871 Da / Num. of mol.: 2 / Mutation: D183A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: Pet11D / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein buffer: 50 mM bicine; pH 8,5; 0.1 mM MnCl2; 1.4 mM ABH. Resevoir:12-25% (wt/vol) jeffamine ED-2001; 0.1 M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 36884 / % possible obs: 98.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 3717 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2aeb Resolution: 2.1→45.38 Å / Stereochemistry target values: Engh & Huber Details: The deposited structure factors are untwinned and have been used as such during refinement. Twinning fraction = 0.5 and twinning operator: -H, -K, L.
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Refinement step | Cycle: LAST / Resolution: 2.1→45.38 Å
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree: 0.324 / Rfactor Rwork: 0.266 |