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Yorodumi- PDB-2pha: Crystal structure of native, unliganded human arginase at 1.90 re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pha | ||||||
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Title | Crystal structure of native, unliganded human arginase at 1.90 resolution | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / PROTON WIRE | ||||||
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: 1.9 Å | ||||||
Authors | Di Costanzo, L. / Pique, M.E. / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pha.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pha.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 2pha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2pha ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2pha | HTTPS FTP |
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-Related structure data
Related structure data | 2phoC 2zavC 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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3 |
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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) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: 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: 48.38 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18-22% Jeffamine ED-2001, 0.1M Hepes (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
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→39.3 Å / Num. all: 49544 / Num. obs: 49544 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7103 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AEB Resolution: 1.9→18.03 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: From 39.3 and 18.03 A there are only very few reflections and the scaling process doesn't record those in the output file of structure factors because those have a poor profile. The data is ...Details: From 39.3 and 18.03 A there are only very few reflections and the scaling process doesn't record those in the output file of structure factors because those have a poor profile. The data is perfect hemihedral twinning with twinning operator: -h,-k,l and twinned fraction:0.5
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Refinement step | Cycle: LAST / Resolution: 1.9→18.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2 Å / Rfactor Rfree: 0.314 / Rfactor Rwork: 0.305 |