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Yorodumi- PDB-3aqy: Crystal structure of Plodia interpunctella beta-GRP/GNBP3 N-termi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aqy | ||||||
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Title | Crystal structure of Plodia interpunctella beta-GRP/GNBP3 N-terminal domain | ||||||
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: 1.58 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 | 3aqy.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aqy.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 3aqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aqy_validation.pdf.gz | 429.6 KB | Display | wwPDB validaton report |
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Full document | 3aqy_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 3aqy_validation.xml.gz | 11 KB | Display | |
Data in CIF | 3aqy_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/3aqy ftp://data.pdbj.org/pub/pdb/validation_reports/aq/3aqy | HTTPS FTP |
-Related structure data
Related structure data | 3aqxSC 3aqzC 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: 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: 2.05 Å3/Da / Density % sol: 40.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M ammonium sulfate, 0.1M MES, 30% w/v PEG 5000 MME, pH 6.5, 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: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 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: 1.57→50 Å / Num. all: 27915 / Num. obs: 27224 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1162 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AQX Resolution: 1.58→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.769 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R Free: 0.103 / 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: 20.416 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.621 Å / Total num. of bins used: 20
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