+Open data
-Basic information
Entry | Database: PDB / ID: 3nt8 | ||||||
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Title | Crystal Structure of Na-ASP-1 | ||||||
Components | Ancylostoma secreted protein 1 | ||||||
Keywords | IMMUNE SYSTEM / PATHOGENESIS RELATED-1 PROTEIN / CYSTEINE-RICH SECRETORY PROTEIN / CAP DOMAIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Necator americanus (New World hookworm) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Asojo, O.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nt8.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nt8.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/3nt8 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/3nt8 | HTTPS FTP |
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-Related structure data
Related structure data | 1u53S S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Necator americanus (New World hookworm) Strain: NECATOR AMERICANUS / Gene: asp1, Human hookworm 51031 / Plasmid: PPICZALPHANA-ASP-1 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: O76744 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å | |||||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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