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Yorodumi- PDB-3mfv: Crystal structure of human arginase I in complex with 2-aminohomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mfv | ||||||
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Title | Crystal structure of human arginase I in complex with 2-aminohomohistidine | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Manganese coordination / structure based design / inhibition / 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 / 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: 1.9 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: 2-aminoimidazole amino acids as inhibitors of the binuclear manganese metalloenzyme human arginase I. Authors: Ilies, M. / Di Costanzo, L. / North, M.L. / Scott, J.A. / 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 | 3mfv.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mfv.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mfv_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 3mfv_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 3mfv_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 3mfv_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/3mfv ftp://data.pdbj.org/pub/pdb/validation_reports/mf/3mfv | HTTPS FTP |
-Related structure data
Related structure data | 3mfwC 2zavS 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 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: pET11-d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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: 48.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 3 uL of protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM AHH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 28% Jeffamine] were equilibrated against a ...Details: 3 uL of protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM AHH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 28% Jeffamine] were equilibrated against a 1 mL reservoir of precipitant solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 50344 / Num. obs: 50344 / % possible obs: 99.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.9→1.99 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.31 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZAV Resolution: 1.9→50 Å Details: THE STRUCTURE IS AFFECTED BY PERFECT HEMIHEDRAL TWINNING. DATA HAVE BEEN USED WITH NO PRIOR DETWINNING. TWIN LAW: -H,-K,L; TWIN FRACTION=0.5
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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