+Open data
-Basic information
Entry | Database: PDB / ID: 4fci | ||||||
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Title | Crystal Structure of the Mn2+2-Human Arginase I-AGPA Complex | ||||||
Components | Arginase-1 | ||||||
Keywords | Hydrolase/Hydrolase inhibitor / Arginase Fold / Hydrolase / 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 / 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: 1.82 Å | ||||||
Authors | D'Antonio, E.L. / Christianson, D.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Binding of the unreactive substrate analog L-2-amino-3-guanidinopropionic acid (dinor-L-arginine) to 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 | 4fci.cif.gz | 134.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fci.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/4fci ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fci | HTTPS FTP |
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-Related structure data
Related structure data | 4fckC 2aebS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34779.879 Da / Num. of mol.: 2 / Fragment: Human Arginase I 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: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GPA / | #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: 2.39 Å3/Da / Density % sol: 48.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: An unliganded Mn2+2-HAI crystal was soaked in 50 mM AGPA, 5 mM MnCl2, 100 mM bicine (pH 8.5), 32% (v/v) Jeffamine ED-2001 for 21 hours, 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: Nov 11, 2011 Details: Cryogenically cooled double crystal monochromater with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror. |
Radiation | Monochromator: Sagitally focused Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 18.056 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 9.313 / Rsym value: 0.183 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2AEB Resolution: 1.82→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: 25 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.82→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.89 Å
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