- PDB-6u6v: Crystal structure of human PD-1H / VISTA -
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Open data
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Basic information
Entry
Database: PDB / ID: 6u6v
Title
Crystal structure of human PD-1H / VISTA
Components
V-type immunoglobulin domain-containing suppressor of T-cell activation
Keywords
IMMUNE SYSTEM / T cell co-inhibition / immunoglobulin-like
Function / homology
Function and homology information
positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production ...positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / endopeptidase activator activity / regulation of immune response / positive regulation of cell migration / positive regulation of gene expression / enzyme binding / identical protein binding / plasma membrane Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interest
N
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 1.71 Å3/Da / Density % sol: 28.18 %
Crystal grow
Temperature: 298 K / Method: microbatch / pH: 6 Details: 0.3 ul protein in HBS with 0.3 ul of crystallization buffer consisting of 100 mM Bis-Tris:HCl pH 6.0 and 28% (v/v) polyethylene glycol monomethyl ether (MW 2000) (Sigma-Aldrich) under a drop ...Details: 0.3 ul protein in HBS with 0.3 ul of crystallization buffer consisting of 100 mM Bis-Tris:HCl pH 6.0 and 28% (v/v) polyethylene glycol monomethyl ether (MW 2000) (Sigma-Aldrich) under a drop of paraffin oil and silicon oil in a 2:1 ratio
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.498 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.175 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2498
531
5.3 %
RANDOM
Rwork
0.2074
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obs
0.2097
9503
95.24 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
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