[English] 日本語
Yorodumi- PDB-2zav: Arginase I (homo sapiens): native and unliganded structure at 1.7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zav | ||||||
---|---|---|---|---|---|---|---|
Title | Arginase I (homo sapiens): native and unliganded structure at 1.70 A resolution | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / Manganese cluster coordination / proton wire / apical water / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Metal-binding / Phosphorylation / Polymorphism / 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 / 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: 1.7 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Crystal structure of human arginase I complexed with thiosemicarbazide reveals an unusual thiocarbonyl mu-sulfide ligand in the binuclear manganese cluster Authors: Di Costanzo, L. / Pique, M.E. / Christianson, D.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zav.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zav.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/2zav ftp://data.pdbj.org/pub/pdb/validation_reports/za/2zav | HTTPS FTP |
---|
-Related structure data
Related structure data | 2phaC 2phoC 2aebS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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) / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.87 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: 14% JEFFAMINE 2001, 0.1M HEPES pH 7.0, 50mM BICINE pH 8.5, 1.4mM Tymine, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.004 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.004 Å / Relative weight: 1 |
Reflection twin | Type: merohedral / Operator: -h,-k,l / Fraction: 0.5 |
Reflection | Resolution: 1.7→50 Å / Num. all: 68183 / Num. obs: 68183 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.52 / Num. unique all: 7000 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AEB: chain A Resolution: 1.7→50 Å / σ(I): 0 Details: Used weighted full matrix least squares procedure. the data diffraction is affect by perfect twinning, twin fraction: 0.5; operator: -h,-k,l The structure factor file is raw data file.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
| ||||||||||||||||||||
Refine LS restraints |
|