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- PDB-5nth: Structure of Leucyl aminopeptidase from Leishmania major in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nth | ||||||
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Title | Structure of Leucyl aminopeptidase from Leishmania major in complex with actinonin | ||||||
![]() | Putative aminopeptidase | ||||||
![]() | HYDROLASE / M17 leucyl aminopeptidase / aminopeptidase / leishmania major actinonin | ||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloaminopeptidase activity / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Timm, J. / Wilson, K. | ||||||
![]() | ![]() Title: Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation inTrypanosoma brucei. Authors: Timm, J. / Valente, M. / Garcia-Caballero, D. / Wilson, K.S. / Gonzalez-Pacanowska, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.3 KB | Display | ![]() |
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PDB format | ![]() | 85.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 737.5 KB | Display | ![]() |
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Full document | ![]() | 739.8 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nskSC ![]() 5nsmC ![]() 5nsqC ![]() 5ntdC ![]() 5ntfC ![]() 5ntgC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 57272.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4QH17, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases | ||||
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#2: Chemical | ChemComp-BCT / | ||||
#3: Chemical | #4: Chemical | ChemComp-BB2 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.8 M Succinic acid pH 7.0, 3 % (w/v) 1,5-Diamino-pentane di-hydrochloride, 5 mM MnSO4, 5 mM actinonin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97781 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→38.11 Å / Num. obs: 21850 / % possible obs: 87.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2 / % possible all: 90.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NSK Resolution: 2.5→38.11 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 12.4 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.285 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.765 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→38.11 Å
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Refine LS restraints |
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