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Open data
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Basic information
Entry | Database: PDB / ID: 3nt8 | ||||||
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Title | Crystal Structure of Na-ASP-1 | ||||||
![]() | Ancylostoma secreted protein 1 | ||||||
![]() | IMMUNE SYSTEM / PATHOGENESIS RELATED-1 PROTEIN / CYSTEINE-RICH SECRETORY PROTEIN / CAP DOMAIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Asojo, O.A. | ||||||
![]() | ![]() Title: Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus. Authors: Asojo, O.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.4 KB | Display | ![]() |
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PDB format | ![]() | 131.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.4 KB | Display | ![]() |
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Full document | ![]() | 436.7 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 47.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1u53S S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45784.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NECATOR AMERICANUS / Gene: asp1, Human hookworm 51031 / Plasmid: PPICZALPHANA-ASP-1 / Production host: ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 3UL (7.5 MG/ML) PROTEIN AND 1.5UL RESERVOIR SOLUTION CONTAINING 21% (W/V) PEG 6000 AND 200 MM, SODIUM CITRATE PH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K | |||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2003 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.15→30.8 Å / Num. obs: 37195 / % possible obs: 93.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.107 / Rsym value: 0.115 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 4.7 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1U53 Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.185 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.318 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.202 Å / Total num. of bins used: 20
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