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Open data
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Basic information
Entry | Database: PDB / ID: 3vat | ||||||
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Title | Crystal structure of DNPEP, ZnMg form | ||||||
![]() | Aspartyl aminopeptidase | ||||||
![]() | HYDROLASE / alpha-beta-alpha sandwich / aspartyl aminopeptidase / binuclear metal center / M18 peptidase / MH clan / tetrahedral aminopeptidase | ||||||
Function / homology | ![]() aspartyl aminopeptidase / metalloaminopeptidase activity / proteolysis / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kiser, P.D. / Chen, Y. / Palczewski, K. | ||||||
![]() | ![]() Title: Insights into substrate specificity and metal activation of Mammalian tetrahedral aspartyl aminopeptidase. Authors: Chen, Y. / Farquhar, E.R. / Chance, M.R. / Palczewski, K. / Kiser, P.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 | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 84.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.3 KB | Display | ![]() |
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Full document | ![]() | 424.9 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3varSC 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: 55039.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.41 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG400, 100 mM Tris-HCl, pH 8.5, 0.2 M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. all: 36800 / Num. obs: 36800 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.127 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.73 / Rsym value: 0.953 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3VAR Resolution: 2.1→73.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.478 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 21.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→73.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.156 Å / Total num. of bins used: 20
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