0 Å resolution at 100 K using a Rigaku FR-E generator and an HTC detector at 45 kV and Histone Methyltransferase inhibitor & PRMT inhibitor 45 mA with Cu Kα radiation at Rigaku MSC (The Woodlands, TX). The crystals belonged
to the space group P3121 with the unit cell parameters a = b = 119.97 Å, c = 118.10 Å, α = β = 90° and γ = 120°. The data were processed and merged using the HKL package version 1.96.6 [63]. Data collection and processing statistics are listed in Table 1. Structure determination and refinement The structure of AlrSP was solved by molecular replacement using CNS version 1.1 [42]. AlrGS (PDB ID 1SFT) [29] without the PLP cofactor was used as a search model, and two monomers per asymmetric unit were assumed, as Lazertinib datasheet suggested by a Matthews selleck compound coefficient [64] of 3.0 with a solvent content of 59.0%. Cross-rotation and translation searches were completed and the best solution was used as an initial model for model building. After rigid body refinement in CNS, ARP/wARP version 6.1 [65] was used to trace the initial protein model and build side chains. Further refinement was carried out using simulated annealing and conjugation gradient minimization. When 97% of residues were built, the co-factor PLP and the carbamylated lysine were placed, and positional
and B-factor refinements were continued resulting in an R and Rfree of 31.9 and 33.9%, respectively. Water molecules were added using the water-picking script in CNS, and further cycles of positional and Biso refinements brought the R and Rfree to 20.7 and 25.7%, respectively. Since previous alanine racemase structures have shown indications of subdomain movement, we tried TLS refinement [43]. We used the TLS motion determination server [66, 67] to produce modified PDB files Amobarbital and TLS input files for the structure partitioned into either one, five or twenty TLS groups, then further refined these models in Refmac5 version 5.5.0109 [44]. All models resulted in similar improvements in R and Rfree so we used the simplest
option, which treated all protein atoms found in the asymmetric unit as a single rigid body (one TLS group). PLP and Lys40 were replaced with an LLP residue (PLP covalently bound to lysine), and TLS refinement was completed using Refmac5. The final model has an R and Rfree of 16.8 and 20.0%, respectively. Refinement statistics are listed in Table 1. Structure factors and final atomic coordinates for AlrSP have been deposited in the Protein Databank (PDB ID: 3S46). B-factor values and correlation coefficients were calculated using the programs Baverage and Overlapmap from the CCP4 suite [44]. Structural and sequence comparisons The multiple structure-based sequence alignment and structural superpositions of AlrSP with closely related structures were performed using the protein structure comparison service (SSM) at the European Bioinformatics Institute (http://www.ebi.ac.uk/msd-srv/ssm) [68].