+Open data
-Basic information
Entry | Database: PDB / ID: 3e8q | ||||||
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Title | X-ray structure of rat arginase I-T135A: the unliganded complex | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / amino acid recognition / mutant T135A / Arginine metabolism / Cytoplasm / Manganese / Metal-binding / Phosphoprotein / Urea cycle | ||||||
Function / homology | Function and homology information regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / arginine metabolic process / negative regulation of T-helper 2 cell cytokine production / response to selenium ion / arginase / arginine catabolic process to ornithine ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / arginine metabolic process / negative regulation of T-helper 2 cell cytokine production / response to selenium ion / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / response to methylmercury / response to vitamin A / response to herbicide / response to steroid hormone / response to manganese ion / Neutrophil degranulation / response to zinc ion / negative regulation of type II interferon-mediated signaling pathway / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / response to axon injury / maternal process involved in female pregnancy / response to vitamin E / cellular response to interleukin-4 / response to amino acid / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / cellular response to dexamethasone stimulus / liver development / female pregnancy / lung development / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / adaptive immune response / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to lipopolysaccharide / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Shishova, E.Y. / Di Costanzo, L. / Emig, F.A. / Ash, D.E. / 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 | 3e8q.cif.gz | 181.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e8q.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/3e8q ftp://data.pdbj.org/pub/pdb/validation_reports/e8/3e8q | HTTPS FTP |
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-Related structure data
Related structure data | 3e6kC 3e6vC 3e8zC 3e9bC 1rlaS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34989.070 Da / Num. of mol.: 3 / Mutation: T135A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arg1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07824, arginase #2: Chemical | ChemComp-MN / #3: 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: 2.12 Å3/Da / Density % sol: 41.92 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: drops containing 3 microL of protein solution [5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM BEC, 2 mM MnCl2] and 3 microL of precipitant solution [0.1 M CHES (pH 9.5), 20% PEG 3350, 0.2 M ...Details: drops containing 3 microL of protein solution [5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM BEC, 2 mM MnCl2] and 3 microL of precipitant solution [0.1 M CHES (pH 9.5), 20% PEG 3350, 0.2 M NaCl] were equilibrated over a 1 mL reservoir of precipitant solution, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / 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: 2.9→50 Å / Num. all: 18754 / Num. obs: 18754 / % possible obs: 96.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1644 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RLA Resolution: 2.9→25.13 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1586605.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.6956 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→25.13 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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