Intensity data collection.X-ray Intensity Data Collection and ProcessingCrystals of CPGRP-S

Intensity data collection.X-ray Intensity Data Collection and ProcessingCrystals of CPGRP-S were stabilized by the addition of 30 glycerol for data collection at low temperature. A single crystal was mounted in a nylon loop and flash-frozen in liquid nitrogen at 100 K. A complete data set was collected using the DBTsponsored MX beamline, BM14 at ESRF, Grenoble, France with ?a wavelength of, l = 0.98 A on 165 mm MAR CCD detector (MAR RESEARCH, Norderstedt, Germany). The data were processed with AUTOMAR and SCALEPACK from HKL package [13]. The results of data collection are given in Table 1.the C and A contacts. LPS molecule was fitted into the electron density on Site-1 at the C contact while SA was fitted in Site-2 at A contact (Figure 1). The coordinates of atoms of both ZK-36374 manufacturer ligands were added to the model in the further cycles of refinement with isotropic B-factors. At this stage, the positions of 256 water oxygen atoms were also obtained from the difference Fourier map. These were added in the subsequent cycles of refinement. The water oxygen atoms were removed from the ?model if they were closer than 2.3 A from the nearest atom. They ?were also removed if they were farther than 3.5 A or if the electron densities at these locations fell below 2.5 s. The refinement converged with values of final Rcryst and Rfree factors of 22.9 and 26.6 respectively. As indicated by calculations using program PROCHECK [17], 90.2 residues were found in the most favoured regions of the Ramachandran’s w, y map [18] while 9.8 residues were found in the additionally allowed regions. The details of refinement parameters are given in Table 1.Results Binding AnalysisThe binding studies of CPGRP-S using SPR were carried out with both ligands, LPS and SA. It has been shown by previous structural studies of binary complexes of CPGRP-S with LPS and SA [9?1] that LPS bound to CPGRP-S in the binding Site-1 at the C contact while SA was found to bind the protein in the binding Site-2 at the A contact [19]. Since the two binding sites were located distantly from each other, the surface plasmon resonance studies were carried out with both ligands separately as well as one after the other. As the protein was immobilized on the chip, LPS was injected onto it at a flow rate of 10 ml/min. It showed binding with final RU of 108. 23727046 Then SA was injected to the LPS-bound protein at the same flow rate. It showed binding with final RU of 76. The binding experiment was also carried out in the reverse order which also showed similar RU values. As seen from the sensogram (Figure 2) both compounds bound to the protein. Since the bindings of SA to LPS-bound protein as well as that of LPS to SA-bound protein occurred, the formation of ternary complex was clearly established.Structure Determination and RefinementThe structure of the ternary complex of CPGRP-S formed with LPS and SA was refined using the structure of native CPGRP-S (PDB Code: 3C2X) (8) as the starting model. The structure consisted of four crystallographically independent protein molecules which were designated as A, B, C and D. The refinement for ?the data to 2.8 A resolution was carried out with program REFMAC 5.5 [14]. The model was improved by repeated 6R-Tetrahydro-L-biopterin dihydrochloride biological activity manual model buildings using program O [15] and Coot [16]. The tight main-chain and side-chain non-crystallographic symmetry restraints between the four molecules were used in the refinement. The electron density maps (2Fo2Fc) and (Fo2Fc) were calculated to adj.Intensity data collection.X-ray Intensity Data Collection and ProcessingCrystals of CPGRP-S were stabilized by the addition of 30 glycerol for data collection at low temperature. A single crystal was mounted in a nylon loop and flash-frozen in liquid nitrogen at 100 K. A complete data set was collected using the DBTsponsored MX beamline, BM14 at ESRF, Grenoble, France with ?a wavelength of, l = 0.98 A on 165 mm MAR CCD detector (MAR RESEARCH, Norderstedt, Germany). The data were processed with AUTOMAR and SCALEPACK from HKL package [13]. The results of data collection are given in Table 1.the C and A contacts. LPS molecule was fitted into the electron density on Site-1 at the C contact while SA was fitted in Site-2 at A contact (Figure 1). The coordinates of atoms of both ligands were added to the model in the further cycles of refinement with isotropic B-factors. At this stage, the positions of 256 water oxygen atoms were also obtained from the difference Fourier map. These were added in the subsequent cycles of refinement. The water oxygen atoms were removed from the ?model if they were closer than 2.3 A from the nearest atom. They ?were also removed if they were farther than 3.5 A or if the electron densities at these locations fell below 2.5 s. The refinement converged with values of final Rcryst and Rfree factors of 22.9 and 26.6 respectively. As indicated by calculations using program PROCHECK [17], 90.2 residues were found in the most favoured regions of the Ramachandran’s w, y map [18] while 9.8 residues were found in the additionally allowed regions. The details of refinement parameters are given in Table 1.Results Binding AnalysisThe binding studies of CPGRP-S using SPR were carried out with both ligands, LPS and SA. It has been shown by previous structural studies of binary complexes of CPGRP-S with LPS and SA [9?1] that LPS bound to CPGRP-S in the binding Site-1 at the C contact while SA was found to bind the protein in the binding Site-2 at the A contact [19]. Since the two binding sites were located distantly from each other, the surface plasmon resonance studies were carried out with both ligands separately as well as one after the other. As the protein was immobilized on the chip, LPS was injected onto it at a flow rate of 10 ml/min. It showed binding with final RU of 108. 23727046 Then SA was injected to the LPS-bound protein at the same flow rate. It showed binding with final RU of 76. The binding experiment was also carried out in the reverse order which also showed similar RU values. As seen from the sensogram (Figure 2) both compounds bound to the protein. Since the bindings of SA to LPS-bound protein as well as that of LPS to SA-bound protein occurred, the formation of ternary complex was clearly established.Structure Determination and RefinementThe structure of the ternary complex of CPGRP-S formed with LPS and SA was refined using the structure of native CPGRP-S (PDB Code: 3C2X) (8) as the starting model. The structure consisted of four crystallographically independent protein molecules which were designated as A, B, C and D. The refinement for ?the data to 2.8 A resolution was carried out with program REFMAC 5.5 [14]. The model was improved by repeated manual model buildings using program O [15] and Coot [16]. The tight main-chain and side-chain non-crystallographic symmetry restraints between the four molecules were used in the refinement. The electron density maps (2Fo2Fc) and (Fo2Fc) were calculated to adj.

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