+Open data
-Basic information
Entry | Database: PDB / ID: 5xz4 | |||||||||
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Title | The X-tay structure of Bumblebee PGRP-SA | |||||||||
Components | Bumblebee peptidoglycan recognition protein SA | |||||||||
Keywords | IMMUNE SYSTEM / Bumblebee / PGRP-SA | |||||||||
Function / homology | Function and homology information N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / peptidoglycan catabolic process / innate immune response / zinc ion binding Similarity search - Function | |||||||||
Biological species | Bombus (bumble bees) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | |||||||||
Authors | Liu, Y.J. / Huang, J.X. / Zhao, X.M. / An, J.D. | |||||||||
Funding support | China, 2items
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Citation | Journal: J Immunol. / Year: 2019 Title: Structural Insights into the Preferential Binding of PGRP-SAs from Bumblebees and Honeybees to Dap-Type Peptidoglycans Rather than Lys-Type Peptidoglycans. Authors: Liu, Y.J. / Zhao, X.M. / Huang, J.X. / Chen, M.M. / An, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xz4.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xz4.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/5xz4 ftp://data.pdbj.org/pub/pdb/validation_reports/xz/5xz4 | HTTPS FTP |
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-Related structure data
Related structure data | 1s2jS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19276.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombus (bumble bees) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSL6*PLUS #2: Chemical | #3: Chemical | ChemComp-TRS / | #4: 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: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→50 Å / Num. obs: 72461 / % possible obs: 96.6 % / Redundancy: 7.5 % / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.41→1.45 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.619 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S2J Resolution: 1.41→38.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.458 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.013
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.276 Å2
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Refinement step | Cycle: 1 / Resolution: 1.41→38.61 Å
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Refine LS restraints |
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