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- PDB-5zee: Crystal structure of Entamoeba histolytica Arginase in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zee | ||||||
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Title | Crystal structure of Entamoeba histolytica Arginase in complex with N(omega)-hydroxy-L-arginine (NOHA) at 1.74 A | ||||||
![]() | Arginase | ||||||
![]() | HYDROLASE/INHIBITOR / Metalloenzyme / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / manganese ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malik, A. / Dalal, V. / Ankri, S. / Tomar, S. | ||||||
![]() | ![]() Title: Structural insights into Entamoeba histolytica arginase and structure-based identification of novel non-amino acid based inhibitors as potential antiamoebic molecules. Authors: Malik, A. / Dalal, V. / Ankri, S. / Tomar, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.7 KB | Display | ![]() |
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PDB format | ![]() | 204.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.8 KB | Display | ![]() |
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Full document | ![]() | 471.3 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 39.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zefC ![]() 5zehC ![]() 1cevS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 294 / Label seq-ID: 17 - 310
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Components
#1: Protein | Mass: 34826.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 35.95 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M bistris propane (pH- 6.5), 0.2M potassium thiocyanate, 22% Peg 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Nov 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→45.14 Å / Num. obs: 55347 / % possible obs: 99.4 % / Redundancy: 5.72 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.58 |
Reflection shell | Resolution: 1.74→1.84 Å / Mean I/σ(I) obs: 2.1 / CC1/2: 0.98 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CEV Resolution: 1.74→45.14 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 7.663 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.828 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→45.14 Å
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Refine LS restraints |
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