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- PDB-1p8m: Structural and Functional Importance of First-Shell Metal Ligands... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p8m | ||||||
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Title | Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. | ||||||
![]() | Arginase 1 | ||||||
![]() | HYDROLASE / UREA CYCLE / BINUCLEAR MANGANESE CLUSTER | ||||||
Function / homology | ![]() regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / arginine metabolic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / response to selenium ion / arginase activity ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / arginine metabolic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / response to selenium ion / arginase activity / arginine catabolic process to ornithine / negative regulation of type II interferon-mediated signaling pathway / 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 / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / response to axon injury / response to vitamin E / response to amino acid / maternal process involved in female pregnancy / cellular response to interleukin-4 / cellular response to dexamethasone stimulus / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / lung development / liver development / female pregnancy / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / adaptive immune response / mitochondrial outer membrane / response to lipopolysaccharide / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cama, E. / Emig, F.A. / Ash, E.-D. / Christianson, D.W. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.5 KB | Display | ![]() |
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PDB format | ![]() | 150 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1p8nC ![]() 1p8oC ![]() 1p8pC ![]() 1p8qC ![]() 1p8rC ![]() 1p8sC ![]() 1rlaS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34048.891 Da / Num. of mol.: 3 / Fragment: Arginase I / Mutation: D128E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, Bicine, Manganese Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2002 / 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: 2.84→30 Å / Num. all: 24715 / Num. obs: 23974 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 6.9 / Num. unique all: 2409 / % possible all: 98.2 |
Reflection shell | *PLUS % possible obs: 98.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RLA Resolution: 2.84→28.97 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 16.5063 Å2 / ksol: 0.278067 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.84→28.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.84→3.02 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.2981 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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