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Yorodumi- PDB-2aeb: Crystal structure of human arginase I at 1.29 A resolution and ex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aeb | ||||||
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Title | Crystal structure of human arginase I at 1.29 A resolution and exploration of inhibition in immune response. | ||||||
Components | Arginase 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / BINUCLEAR MANGANESE CLUSTER / BORONIC ACID INHIBITOR / PERFECTLY TWINNED CRYSTAL / 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 / FOURIER SYNTHESIS / Resolution: 1.29 Å | ||||||
Authors | Di Costanzo, L. / Sabio, G. / Mora, A. / Rodriguez, P.C. / Ochoa, A.C. / Centeno, F. / Christianson, D.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Crystal structure of human arginase I at 1.29 A resolution and exploration of inhibition in the immune response. Authors: Di Costanzo, L. / Sabio, G. / Mora, A. / Rodriguez, P.C. / Ochoa, A.C. / Centeno, F. / Christianson, D.W. #1: Journal: Biochemistry / Year: 2003 Title: Human arginase II: crystal structure and physiological role in male and female sexual arousal Authors: Cama, E. / Colleluori, D.M. / Emig, F.A. / Shin, H. / Kim, S.W. / Kim, N.N. / Traish, A.M. / Ash, D.E. / Christianson, D.W. #2: Journal: Nat.Struct.Biol. / Year: 1999 Title: Arginase-Boronic Acid Complex Highlights a Physiological Role in Erectile Function Authors: Cox, J.D. / Kim, N.N. / Traish, A.M. / 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 | 2aeb.cif.gz | 244.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aeb.ent.gz | 196.7 KB | Display | PDB format |
PDBx/mmJSON format | 2aeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/2aeb ftp://data.pdbj.org/pub/pdb/validation_reports/ae/2aeb | HTTPS FTP |
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-Related structure data
Related structure data | 1wvaC 1d3vS 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) / 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: 2.41 Å3/Da / Density % sol: 49.04 % / Description: DATA WERE SCALED AS SG P3. |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: PegMME 5000, Bis Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K, pH 7.10 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9124 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9124 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→50 Å / Num. obs: 150499 / % possible obs: 92.7 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.29→1.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.85 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1D3V Highest resolution: 1.29 Å Details: DUE TO POORLY DEFINED DENSITY, THE FOLLOWING RESIDUES: A5, A48 (NZ), A222 (SIDE CHAINS), B41 (SIDE CHAINS), B48 (SIDE CHAINS), B89 (NZ), B222 (SIDE CHAINS) AND B224 (SIDE CHAINS) HAVE BEEN ...Details: DUE TO POORLY DEFINED DENSITY, THE FOLLOWING RESIDUES: A5, A48 (NZ), A222 (SIDE CHAINS), B41 (SIDE CHAINS), B48 (SIDE CHAINS), B89 (NZ), B222 (SIDE CHAINS) AND B224 (SIDE CHAINS) HAVE BEEN MODELED AT MINOR OCCUPANCY. BECAUSE PART OF A DISORDERED SIDE CHAINS, RESIDUES A83 AND B217 HAVE DISORDERED DENSITY. THEREFORE, HYDROGENS ARE NOT PLACED IN THE SIDECHAINS OF THESE TWO RESIDUE. REFINED TWIN FRACTIONS: 0.46. TWIN OPERATOR: -H, -K, L
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Refinement step | Cycle: LAST / Highest resolution: 1.29 Å
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Refine LS restraints |
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