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Yorodumi- PDB-3lp4: Crystal structure of human arginase I in complex with L-LYSINE, 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lp4 | ||||||
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Title | Crystal structure of human arginase I in complex with L-LYSINE, 1.90A Resolution. | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / LYSINE INHIBITION / MANGANESE CLUSTER / Arginine metabolism / Cytoplasm / Manganese / Metal-binding / 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: 1.9 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2010 Title: Inhibition of human arginase I by substrate and product analogues. Authors: Di Costanzo, L. / Ilies, M. / Thorn, K.J. / 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 | 3lp4.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lp4.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lp4_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 3lp4_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 3lp4_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 3lp4_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/3lp4 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/3lp4 | HTTPS FTP |
-Related structure data
Related structure data | 3kv2C 3lp7C 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
#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 / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
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Crystal grow | Method: vapor diffusion, hanging drop Details: 0.1 M bis-Tris pH 6.5, 28% PEGMME 2000. Crystals were harvested and soaked in a precipitant solution augmented with 20 mM L-lysine. Cryoprotected in 32% Jeffamine, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 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. obs: 49010 / % possible obs: 97.1 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.9→2.01 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.5 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2ZAV Resolution: 1.9→34.2 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→34.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å
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