+Open data
-Basic information
Entry | Database: PDB / ID: 3tf3 | ||||||
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Title | Crystal structure of metal-free Human Arginase I | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / ARGINASE FOLD | ||||||
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 / arginine catabolic process to ornithine / arginase / arginase activity / 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 / arginine catabolic process to ornithine / arginase / arginase activity / 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: 1.64 Å | ||||||
Authors | D'Antonio, E.L. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Crystal structures of complexes with cobalt-reconstituted human arginase I. Authors: D'Antonio, E.L. / 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 | 3tf3.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tf3.ent.gz | 102.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/3tf3 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tf3 | HTTPS FTP |
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-Related structure data
Related structure data | 3th7C 3theC 3thhC 3thjC 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: 34779.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pBS(KS) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05089, arginase #2: 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: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES, 30% (v/v) Jeffamine ED-2001, 0.014 M thymine, 0.0001 M manganese chloride. following xtal growth, metal-free HAI crystals are prepared by soaking a single crystal in 0.015 M ...Details: 0.1 M HEPES, 30% (v/v) Jeffamine ED-2001, 0.014 M thymine, 0.0001 M manganese chloride. following xtal growth, metal-free HAI crystals are prepared by soaking a single crystal in 0.015 M dipicolinic acid, 0.015 M EDTA, 30% (v/v) Jeffamine ED-2001 for 1 week, 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: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2010 Details: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 77810 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 35.185 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.459 / Rsym value: 0.43 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AEB Resolution: 1.64→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.64→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.7 Å
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