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Yorodumi- PDB-3aqz: Crystal structure of Plodia interpunctella beta-GRP/GNBP3 N-termi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aqz | |||||||||
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Title | Crystal structure of Plodia interpunctella beta-GRP/GNBP3 N-terminal domain with laminarihexaoses | |||||||||
Components | Beta-1,3-glucan-binding protein | |||||||||
Keywords | SUGAR BINDING PROTEIN / beta-sandwich / Immune receptor / beta-1 / 3-glucan | |||||||||
Function / homology | Function and homology information polysaccharide immune receptor activity / (1->3)-beta-D-glucan binding / lipoteichoic acid binding / lipopolysaccharide immune receptor activity / cell surface pattern recognition receptor signaling pathway / pattern recognition receptor activity / regulation of innate immune response / hydrolase activity, hydrolyzing O-glycosyl compounds / lipopolysaccharide-mediated signaling pathway / lipopolysaccharide binding ...polysaccharide immune receptor activity / (1->3)-beta-D-glucan binding / lipoteichoic acid binding / lipopolysaccharide immune receptor activity / cell surface pattern recognition receptor signaling pathway / pattern recognition receptor activity / regulation of innate immune response / hydrolase activity, hydrolyzing O-glycosyl compounds / lipopolysaccharide-mediated signaling pathway / lipopolysaccharide binding / carbohydrate metabolic process / innate immune response / extracellular region Similarity search - Function | |||||||||
Biological species | Plodia interpunctella (Indianmeal moth) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Kanagawa, M. / Satoh, T. / Ikeda, A. / Adachi, Y. / Ohno, N. / Yamaguchi, Y. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aqz.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aqz.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 3aqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/3aqz ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aqz | HTTPS FTP |
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-Related structure data
Related structure data | 3aqxSC 3aqyC S: Starting model for refinement C: citing same article (ref.) |
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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: 12176.650 Da / Num. of mol.: 2 / Fragment: beta-glucan binding domain, UNP residues 24-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plodia interpunctella (Indianmeal moth) Plasmid: pCold-I(MBP-TRX fusion) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q8MU95 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M Lithium chloride, 20% (v/v) PEG 3350, 5mM laminarihexaose, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2010 |
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: 2.2→50 Å / Num. all: 14108 / Num. obs: 13802 / % possible obs: 97.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1329 / % possible all: 97 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AQX Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.542 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R Free: 0.233 / 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: 24.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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