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- PDB-5ntg: Structure of Leucyl aminopeptidase from Trypanosoma cruzi in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ntg | ||||||
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Title | Structure of Leucyl aminopeptidase from Trypanosoma cruzi in complex with citrate | ||||||
![]() | Aminopeptidase | ||||||
![]() | HYDROLASE / M17 leucyl aminopeptidase / aminopeptidase / tryanosoma cruzi | ||||||
Function / homology | ![]() metalloaminopeptidase activity / manganese ion binding / proteolysis / 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 | ![]() | 209.5 KB | Display | ![]() |
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PDB format | ![]() | 166 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467 KB | Display | ![]() |
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Full document | ![]() | 471.6 KB | Display | |
Data in XML | ![]() | 39.4 KB | Display | |
Data in CIF | ![]() | 56.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nskSC ![]() 5nsmC ![]() 5nsqC ![]() 5ntdC ![]() 5ntfC ![]() 5nthC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 11 - 519 / Label seq-ID: 10 - 518
NCS ensembles :
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Components
#1: Protein | Mass: 55955.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Phosphate-citrate pH 4.2, 40 % (v/v) PEG 300, 5 mM MnSO4, 5 mM amastatin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→57.31 Å / Num. obs: 43546 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.202 / Num. unique obs: 4249 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NSK Resolution: 2.32→57.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.257 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.21 Å2
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Refinement step | Cycle: 1 / Resolution: 2.32→57.31 Å
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Refine LS restraints |
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