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- PDB-4rhk: Crystal structure of T. brucei arginase-like protein in an oxidiz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rhk | ||||||
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Title | Crystal structure of T. brucei arginase-like protein in an oxidized 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 | ![]() | 72.3 KB | Display | ![]() |
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PDB format | ![]() | 56.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.2 KB | Display | ![]() |
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Full document | ![]() | 447 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.7 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38732.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 2% (v/v) tacsimate, pH 7.4, 5% (v/v) 2-propanol, 0.1 M imidazole, 8% 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: Oct 19, 2012 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.38→50 Å / Num. obs: 15468 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 18.1 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 31.429 | |||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: PDB entry 4RHI / Resolution: 2.38→40.657 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 34.93 / Stereochemistry target values: ML
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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: 2.38→40.657 Å
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Refine LS restraints |
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LS refinement shell |
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