+Open data
-Basic information
Entry | Database: PDB / ID: 1wvb | ||||||
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Title | Crystal structure of human arginase I: the mutant E256Q | ||||||
Components | Arginase 1Arginase | ||||||
Keywords | HYDROLASE / TWINNED CRYSTAL / MUTANT E256Q | ||||||
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: 2.3 Å | ||||||
Authors | Di Costanzo, L. / Guadalupe, S. / Mora, A. / Centeno, F. / Christianson, D.W. | ||||||
Citation | Journal: To be Published Title: Crystal structure of human arginase I: the mutant E256Q Authors: Di Costanzo, L. / Guadalupe, S. / Mora, A. / Centeno, F. / Christianson, D.W. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Subunit-subunit interactions in trimeric arginase. Generation of active monomers by mutation of a single amino acid Authors: Lavulo, L.T. / Sossong Jr., T.M. / Brigham-Burke, M.R. / Doyle, M.L. / Cox, J.D. / Christianson, D.W. / Ash, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wvb.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wvb.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 1wvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvb ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvb | HTTPS FTP |
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-Related structure data
Related structure data | 1d3vS 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: 34778.895 Da / Num. of mol.: 2 / Mutation: E256Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-11a / 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEGMME 2000, Bis-tris, ph 6.5(reservoir), pH 8.5(SAMPLE), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 27626 / Num. obs: 27626 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.109 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 28004 / Rsym value: 0.36 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D3V Resolution: 2.3→50 Å / σ(F): 1 / σ(I): 1 Details: This is a twinned structure. The twinning operator is (h,k,l) -> (-h,-k,l) and the twinning fraction is 0.5.
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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