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- PDB-4rhj: Crystal structure of wild-type T. brucei arginase-like protein in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rhj | ||||||
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Title | Crystal structure of wild-type T. brucei arginase-like protein in a reduced form | ||||||
![]() | Arginase | ||||||
![]() | UNKNOWN FUNCTION / Arginase-deacetylase fold | ||||||
Function / homology | ![]() putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / arginine metabolic process / arginase / arginase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hai, Y. / Barrett, M.P. / Christianson, D.W. | ||||||
![]() | ![]() Title: Crystal Structure of an Arginase-like Protein from Trypanosoma brucei That Evolved without a Binuclear Manganese Cluster. Authors: Hai, Y. / Kerkhoven, E.J. / Barrett, M.P. / 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 | ![]() | 342.1 KB | Display | ![]() |
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PDB format | ![]() | 277.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4rhiSC ![]() 4rhkC ![]() 4rhlC ![]() 4rhmC ![]() 4rhqC 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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6 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38732.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.1 M HEPES, pH 7.8, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.49 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. all: 181427 / Num. obs: 181427 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 | |||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4RHI Resolution: 1.8→42.229 Å / σ(F): 1.97 / Phase error: 24.3 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.229 Å
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Refine LS restraints |
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LS refinement shell |
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