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Yorodumi- PDB-1pq3: Human Arginase II: Crystal Structure and Physiological Role in Ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pq3 | ||||||
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Title | Human Arginase II: Crystal Structure and Physiological Role in Male and Female Sexual Arousal | ||||||
Components | Arginase II, mitochondrial precursor | ||||||
Keywords | HYDROLASE / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginase ...negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-17 production / regulation of reactive oxygen species biosynthetic process / ureteric bud development / negative regulation of tumor necrosis factor production / Mitochondrial protein degradation / striated muscle contraction / nitric oxide biosynthetic process / positive regulation of cellular senescence / manganese ion binding / adaptive immune response / mitochondrial matrix / innate immune response / mitochondrion / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
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. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pq3.cif.gz | 362.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pq3.ent.gz | 296.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pq3 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pq3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 33231.656 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78540, arginase |
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-Non-polymers , 5 types, 445 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-S2C / #6: 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: 3.77 Å3/Da / Density % sol: 67.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: Tris, Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: RH-COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 79653 / Num. obs: 75977 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 79653 / % possible obs: 99.3 % / Num. measured all: 404391 / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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LS refinement shell | Resolution: 2.7→2.87 Å
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Refinement | *PLUS Highest resolution: 2.7 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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