Coordinate root mean square deviation

When comparing two proteins, the sets of points can include the only, all backbone atoms, or all atoms of the proteins. Different metrics have been used in the literature to determine the geometric similarity between sets of points. For protein superposition, the most common metric is the coordinate root mean square deviation (cRMS), which is defined as follows ... 

The rule of thumb for a successful application of molecular replacement is that the model should have a root-mean-square deviation (RMSD) on C-alpha coordinates 2.0-2.5 Angstroms with the target structure, corresponding to a sequence identity with the target of 25-35%. In practice, however, there are many more structures solved by MR in the PDB using models with sequence identity of 60% or higher than otherwise. 

Protein PDB code Site Coordinating peptide No. of coordinating ligands No. of coordinating waters No. of bidentate ligands Root mean square deviation of ligands from ideal polygon" (A) j Ca2 + (M)" Reference for affinity data... 

An important question is What is the relationship between percent sequence identity and similarity of tertiary structure This depends on the length of the protein the longer the protein, the lower the percent identity that implies identical structure. For a protein of 85 residues, a 25 to 30% sequence identity implies an identical three-dimensional structure. The more the percent identity of structure, the smaller the root mean square deviation of the coordinates of the two structures34 (Figure 1.21). 

The crystal structures of the E. coli DHFR-methotrexate binary complex (Bolin et al., 1982), of the Lactobacillus casei (DHFR-NADPH-methotrexate ternary complex (Filman et al., 1982), of the human DHFR-folate binary complex (Oefner et al., 1988), and of the mouse (DHFR-NADPH-trimethoprim tertiary complex (Stammers et al., 1987) have been resolved at a resolution of 2 A or better. The crystal structures of the mouse DHFR-NADPH-methotrexate (Stammers et al., 1987) and the avian DHFR—phenyltriazine (Volz et al., 1982) complexes were determined at resolutions of 2.5 and 2.9 A, respectively. Recently, the crystal structure of the E. coli DHFR—NADP + binary and DHFR-NADP+-folate tertiary complexes were resolved at resolutions of 2.4 and 2.5 A, respectively (Bystroff et al., 1990). DHFR is therefore the first dehydrogenase system for which so many structures of different complexes have been resolved. Despite less than 30% homology between the amino acid sequences of the E. coli and the L. casei enzymes, the two backbone structures are similar. When the coordinates of 142 a-carbon atoms (out of 159) of E. coli DHFR are matched to equivalent carbons of the L. casei enzyme, the root-mean-square deviation is only 1.07 A (Bolin et al., 1982). Not only are the three-dimensional structures of DHFRs from different sources similar, but, as we shall see later, the overall kinetic schemes for E. coli (Fierke et al., 1987), L. casei (Andrews et al., 1989), and mouse (Thillet et al., 1990) DHFRs have been determined and are also similar. That the structural properties of DHFRs from different sources are very similar, in spite of the considerable differences in their sequences, suggests that in the absence, so far, of structural information for ADHFR it is possible to assume, at least as a first approximation, that the a-carbon chain of the halophilic enzyme will not deviate considerably from those of the nonhalophilic ones. 

After completion of the calculations182 on poly(Gly-Pro-Pro), it was learned that Okuyama et al.187 had carried out a single-crystal X-ray structure analysis of (Pro—Pro—Gly)10. The calculated structure (Figure 25) is in agreement with theirs, with a root-mean-square deviation of 0.3 A for all (nonhydrogen) atoms, based on a comparison between the X-ray coordinates (kindly provided by Professor M. Kakudo) and the computed coordinates. 

Crystal structures have been determined of several ferrichromes. Most of this work was performed by van der Helm and coworkers. The crystal structures of the members of this siderophore family can be superposed and a root-mean-square deviation of the 49 atoms, which are common to all members, is obtained of approximately 0.30 A. A comparison of the conformational angles around the cyclic hexapeptide ring shows differences of not more than 25°. This indicates that the structures and conformations are not the same but that they are similar with some conformational freedom. In all structures, the iron coordination site is on one side of the molecule, the coordination of the metal is K-cis, and the conformation of the amino acids is L. A (II) bend and a (I) bend of the cyclic peptide skeleton is found. In addition, extensive conformational analyses of siderophores in solution were performed by Lhnas and coworkers employing H andNMR. ... 

Root-mean-square deviation (RMSD) of the coordinates of backbone atoms in the simulated structure from those in the X-ray crystal structiue of BChE. nonpre and pre refer to the non-prereactive and prereactive BChE-cocaine complexes, respectively... 

Table 1. Structural parameters for solvation shell of lithium ion in DMF as determined by XD measurements and least-squares fitting procedure average distances r, , root mean square deviations /y, and coordination numbers ny. Solution of LiQ (left) and of LiNCS (right).

We define R to be the root mean square deviation (RMSD) of the ligand coordinates from the native state, and the native state is chosen to be the reference state, so Rc = 0.0. 

The stability of proteins refers to the maintenance of a defined three-dimensional structure with specific thermodynamic and functional properties. High-resolution structures in the crystalline state and in solution have reached a stage at which the atomic coordinates of proteins can be compared with an accuracy down to root mean square deviation (r.m.s.d.) values less than 1 A. However, even this precision does not allow the fi ee energy of stabilization to be calculated from the coordinates, nor does it allow predictions with respect to the dynamics of functionally relevant local interactions in active or regulatory sites of homologous proteins. The fluctuations between preferred conformations of native proteins involved in such functionally important motions may very well show amplitudes and angles of up to 50 A and 20°, respectively. ... 

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