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- PDB-3rla: ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rla | ||||||
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Title | ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION | ||||||
![]() | ARGINASE | ||||||
![]() | HYDROLASE / UREA CYCLE / ARGININE METABOLISM | ||||||
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 / response to selenium ion / arginase / 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 / response to selenium ion / arginase / arginase activity / arginine catabolic process to ornithine / 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 / response to vitamin E / response to amino acid / maternal process involved in female pregnancy / 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 / adaptive immune response / mitochondrial outer membrane / response to lipopolysaccharide / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Scolnick, L.R. / Kanyo, Z.F. / Christianson, D.W. | ||||||
![]() | ![]() Title: Altering the binuclear manganese cluster of arginase diminishes thermostability and catalytic function. Authors: Scolnick, L.R. / Kanyo, Z.F. / Cavalli, R.C. / 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 | ![]() | 186 KB | Display | ![]() |
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PDB format | ![]() | 148.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.1 KB | Display | ![]() |
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Full document | ![]() | 398 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 34995.051 Da / Num. of mol.: 3 / Mutation: H101N 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: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 12 - 18% PEG 8000, 50 MM BICINE PH = 8.5, 0.05% AZIDE, 1 MM MNCL2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: YALE |
Radiation | Monochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→8 Å / Num. obs: 26381 / % possible obs: 74 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.54→2.6 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.4 / % possible all: 79.5 |
Reflection | *PLUS Num. measured all: 65410 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: RAT LIVER ARGINASE Resolution: 2.54→15 Å / Rfactor Rfree error: 0.0004 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION USED
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Refine analyze | Luzzati d res low obs: 12 Å / Luzzati sigma a obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.54→2.65 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.5 |