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- PDB-3aqx: Crystal structure of Bombyx mori beta-GRP/GNBP3 N-terminal domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3aqx | |||||||||
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Title | Crystal structure of Bombyx mori beta-GRP/GNBP3 N-terminal domain with laminarihexaoses | |||||||||
![]() | Beta-1,3-glucan-binding protein | |||||||||
![]() | SUGAR BINDING PROTEIN / beta-sandwich / Immune receptor / beta-1 / 3-glucan | |||||||||
Function / homology | ![]() polysaccharide immune receptor activity / (1->3)-beta-D-glucan binding / cell surface pattern recognition receptor signaling pathway / pattern recognition receptor activity / regulation of innate immune response / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / innate immune response / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kanagawa, M. / Satoh, T. / Ikeda, A. / Adachi, Y. / Ohno, N. / Yamaguchi, Y. | |||||||||
![]() | ![]() Title: Structural insights into recognition of triple-helical beta-glucans by an insect fungal receptor Authors: Kanagawa, M. / Satoh, T. / Ikeda, A. / Adachi, Y. / Ohno, N. / Yamaguchi, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.8 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aqyC ![]() 3aqzC ![]() 3ie4S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11815.192 Da / Num. of mol.: 2 / Fragment: beta-glucan binding domain, UNP residues 17-118 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M ammonium sulfate, 0.1M HEPES sodium buffer, 10% (w/v) PEG 4000, 5mM laminarihexaose, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 16433 / Num. obs: 16156 / % possible obs: 98.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 2 / Num. unique all: 692 / % possible all: 87.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3IE4 Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.086 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R Free: 0.169 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.777 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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