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- PDB-7dy5: Structure of the ternary complex of peptidoglycan recognition pro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dy5 | |||||||||
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Title | Structure of the ternary complex of peptidoglycan recognition protein-short (PGRP-S) with hexanoic acid and tartaric acid at 2.30A resolution | |||||||||
![]() | Peptidoglycan recognition protein 1 | |||||||||
![]() | IMMUNE SYSTEM / Recognition protein | |||||||||
Function / homology | ![]() peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / negative regulation of cytokine production / detection of bacterium / peptidoglycan catabolic process / defense response to Gram-positive bacterium / innate immune response / zinc ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Maurya, A. / Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P. | |||||||||
![]() | ![]() Title: Structure of the ternary complex of peptidoglycan recognition protein-short (PGRP-S) Authors: Maurya, A. / Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.9 KB | Display | ![]() |
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PDB format | ![]() | 118.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6j3w S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 19011.459 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 433 molecules ![](data/chem/img/TLA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/6NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/6NA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-6NA / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% PEG 3350, 0.2M Sodium potassium tartrate, 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 18, 2018 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50.68 Å / Num. obs: 25883 / % possible obs: 78.01 % / Redundancy: 4.8 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.05 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.3→2.39 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1879 / CC1/2: 0.87 / Rpim(I) all: 0.32 / % possible all: 58 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6J3W ![]() 6j3w Resolution: 2.3→50.68 Å / SU ML: 0.2923 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.0535 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50.68 Å
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Refine LS restraints |
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LS refinement shell |
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