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Open data
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Basic information
Entry | Database: PDB / ID: 7nsz | ||||||
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Title | Drosophila PGRP-LB Y78F mutant | ||||||
![]() | Isoform A of Peptidoglycan-recognition protein LB | ||||||
![]() | IMMUNE SYSTEM / Peptidoglycan recognition protein / PGRP / PGRP-LB / Drosophila | ||||||
Function / homology | ![]() negative regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / negative regulation of peptidoglycan recognition protein signaling pathway / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / peptidoglycan catabolic process / defense response to Gram-positive bacterium / innate immune response / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Orlans, J. / Aller, P. / Da Silva, P. | ||||||
![]() | ![]() Title: PGRP-LB: An Inside View into the Mechanism of the Amidase Reaction. Authors: Orlans, J. / Vincent-Monegat, C. / Rahioui, I. / Sivignon, C. / Butryn, A. / Soulere, L. / Zaidman-Remy, A. / Orville, A.M. / Heddi, A. / Aller, P. / Da Silva, 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 | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nsxC ![]() 7nsyC ![]() 7nt0C ![]() 1ohtS 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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Unit cell |
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Components
#1: Protein | Mass: 23771.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Please can you count the first two residue as -1 and -2 because they belong to the cleavage site of the tag. The number 1 of the sequence would be third residue. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8INK6, N-acetylmuramoyl-L-alanine amidase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 5, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.3→338.94 Å / Num. obs: 42802 / % possible obs: 99.9 % / Redundancy: 31.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.022 / Rrim(I) all: 0.098 / Net I/σ(I): 20.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OHT Resolution: 1.3→56.554 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 0.805 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.056
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.906 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→56.554 Å
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Refine LS restraints |
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LS refinement shell |
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