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Yorodumi- PDB-1p8p: Structural and Functional Importance of First-Shell Metal Ligands... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p8p | ||||||
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Title | Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. | ||||||
Components | Arginase 1Arginase | ||||||
Keywords | HYDROLASE / UREA CYCLE / ARGININE METABOLISM / BINUCLEAR MANGANESE CLUSTER | ||||||
Function / homology | Function and homology information regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginine catabolic process to ornithine / response to selenium ion / arginase ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginine catabolic process to ornithine / response to selenium ion / arginase / arginase activity / urea cycle / response to methylmercury / response to vitamin A / response to herbicide / response to steroid hormone / response to manganese ion / Neutrophil degranulation / response to zinc ion / negative regulation of type II interferon-mediated signaling pathway / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / response to axon injury / maternal process involved in female pregnancy / response to vitamin E / response to amino acid / cellular response to interleukin-4 / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / cellular response to dexamethasone stimulus / liver development / female pregnancy / lung development / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to lipopolysaccharide / adaptive immune response / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Cama, E. / Emig, F.A. / Ash, D.E. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Structural and functional importance of first-shell metal ligands in the binuclear manganese cluster of arginase I Authors: Cama, E. / Emig, F.A. / Ash, D.E. / Christianson, D.W. #1: Journal: Biochemistry / Year: 1997 Title: ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION Authors: Scolnick, L.R. / Kanyo, Z.F. / Cavalli, C.R. / 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 | 1p8p.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p8p.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 1p8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/1p8p ftp://data.pdbj.org/pub/pdb/validation_reports/p8/1p8p | HTTPS FTP |
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-Related structure data
Related structure data | 1p8mC 1p8nC 1p8oC 1p8qC 1p8rC 1p8sC 3rlaS 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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Unit cell |
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-Components
#1: Protein | Mass: 34010.820 Da / Num. of mol.: 3 / Fragment: Arginase I / Mutation: H101N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: ARG1 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: P07824, 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: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 8000, Bicine, Manganese Chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 10, 1995 / Details: Yale mirrors |
Radiation | Monochromator: Yale / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. all: 35468 / Num. obs: 26530 / % possible obs: 74.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RLA Resolution: 2.5→14.89 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.8537 Å2 / ksol: 0.342534 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→14.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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