OMITMAP: An electron density map suitable for the examination of errors in a macromolecular model

Bhat, Talapady N.; Cohen, Gerald

doi:10.1107/s0021889884011456

Cited by 133 publications

(84 citation statements)

References 6 publications

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“…In the later cycles, the cutoff values were reduced to 2.5 and 0.8', respectively. Omit maps (Vijayan, 1980;Bhat & Cohen, 1984), in addition to F o À F c and 2F o À F c maps, were also used in the later stages of re®nement. Bulk-solvent correction and anisotropic scaling were used throughout.…”

Section: Methodsmentioning

confidence: 99%

Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme

Saraswathi

Sankaranarayanan

Vijayan

2002

Acta Crystallogr D Biol Cryst

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In pursuance of a long-range programme on the hydration, mobility and action of proteins, the structural basis of the stabilizing effect of sugars and polyols is being investigated. With two crystallographically independent molecules with slightly different packing environments in the crystal, monoclinic lysozyme constitutes an ideal system for exploring the problem. The differences in the structure and hydration of the two molecules provide a framework for examining the changes caused by stabilizing additives. Monoclinic crystals were grown under native conditions and also in the presence of 10% sucrose, 15% trehalose, 10% trehalose, 10% sorbitol and 5% glycerol. The crystal structures were re®ned at resolutions ranging from 1.8 to 2.1 A Ê . The average B values, and hence the mobility of the structure, are lower in the presence of additives than in the native crystals. However, a comparison of the structures indicates that the effect of the additives on the structure and the hydration shell around the protein molecule is considerably less than that caused by differences in packing. It is also less than that caused by the replacement of NaNO 3 by NaCl as the precipitant in the crystallization experiments. This result is not in conformity with the commonly held belief that additives exert their stabilizing effect through the reorganization of the hydration shell, at least as far as the ordered water molecules are concerned. PDB References: lysozyme, native monoclinic (I), 1lj3, r1lj3sf; native monoclinic (II), 1lj4, r1lj4sf; with 10% sucrose (I), 1lje, r1ljesf; with 10% sucrose (II), 1ljf, r1ljfsf; with 5% glycerol (I), 1ljg, r1ljgsf; with 5% glycerol (II), 1ljh, r1ljhsf; with 10% sorbitol, 1lji, r1ljisf; with 10% trehalose, 1ljj, r1ljjsf; with 15% trehalose, 1ljk, r1ljksf.

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Section: Methodsmentioning

confidence: 99%

Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme

Saraswathi

Sankaranarayanan

Vijayan

2002

Acta Crystallogr D Biol Cryst

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“…Recently, Karle (1991) proposed using 'rolling' working sets to aid the convergence behavior of least-squares minimization. Refined omit maps (Bhat & Cohen, 1984;Hodel, Kim & Brfinger, 1992) can be viewed as the real-space analog to cross validation: part(s) of the model are omitted and then the remaining model is refined.…”

Section: Cross Validation In Macromolecular Crystallographymentioning

confidence: 99%

Assessment of phase accuracy by cross validation: the free R value. Methods and applications

Brünger¹

1993

Acta Crystallogr D Biol Crystallogr

440

324

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Analogies between the free R statistic [Briinger (1992). Nature (London), 355,(472)(473)(474) and the statistical methods of cross validation and bootstrap are discussed. Several new applications which make use of the previously observed correlation between the free R value and the phase accuracy of crystal structures are presented. One application concerns the relative weighting of individual restraint classes in macromolecular refinement. The free R value provides an objective statistical basis for the optimal choice of the weights. The results for the refinement of a penicillopepsin crystal structure at 1.8 A resolution indicate that overall bond length and bond angle weights, derived from uncertainties observed in smallmolecule crystal structures, appear to be transferable to macromolecules. In another application, the landscape of the R value around the crystal structure was investigated for unrestrained modeling of diffraction data with equal atomic scatterers. Others have suggested applications to ab initio phasing because of the simplicity of the liquidlike system of equal atomic scatterers. However, there are a large number of incorrect configurations of the scatterers whose R values at 1.8 A resolution are close to that of the correct configuration given by the positions of the non-hydrogen atoms in the penicillopepsin crystal structure. A substantial number of the incorrect configurations have higher free R values than the correct one. It is therefore conceivable that the free R value could be used as a selection criterion to distinguish between certain incorrect configurations and configurations close to the correct one.

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“…Following refinement in X-PLOR with 8-2.8 8, data, model adjustments were made interactively with the modeling program FRODO (Jones, 1978;Pflugrath et al, 1984) and 2F0 -F, and F, -F, electron density maps displayed on an Evans and Sutherland PS390 graphics workstation. OMITMAPS (Bhat & Cohen, 1984) were calculated to confirm the positions of side chains that differed in sequence between the two proteins and to place the side chains in the flexible FG loop. The electron density for this loop in each monomer was weak and broken.…”

Section: Molecular Replacement and Phase Calculationmentioning

confidence: 99%

Crystal structure of the coat protein from the GA bacteriophage: Model of the unassembled dimer

White

Mitchell

et al. 1996

Protein Science

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There are four groups of RNA bacteriophages with distinct antigenic and physicochemical properties due to differences in surface residues of the viral coat proteins. Coat proteins also play a role as translational repressor during the viral life cycle, binding an RNA hairpin within the genome. In this study, the first crystal structure of the coat protein from a Group I1 phage GA is reported and compared to the Group I MS2 coat protein. The structure of the GA dimer was determined at 2.8 8, resolution (R-factor = 0.20). The overall folding pattern of the coat protein is similar to the Group I MS2 coat protein in the intact virus (Golmohammadi R, Valegird K, Fridborg K, Liljas L, 1993, J Mol Biol234:620-639) or as an unassembled dimer (Ni CZ, Syed R, Kodandapani R, Wickersham J, Peabody DS, Ely KR, 1995, Srructure 3:255-263). The structures differ in the FG loops and in the first turn of the a A helix. GA and MS2 coat proteins differ in sequence at 49 of 129 amino acid residues. Sequence differences that contribute to distinct immunological and physical properties of the proteins are found at the surface of the intact virus in the AB and FG loops. There are six differences in potential RNA contact residues within the RNA-binding site located in an antiparallel @sheet across the dimer interface. Three differences involve residues in the center of this concave site: Lys/Arg 83, Ser/Asn 87, and Asp/Glu 89. Residue 87 was shown by molecular genetics to define RNA-binding specificity by GA or MS2 coat protein (Lim F, Spingola M, Peabody DS, 1994, J BioZ Chem 269:9006-9010). This sequence difference reflects recognition of the nucleotide at position -5 in the unpaired loop of the translational operators bound by these coat proteins. In GA, the nucleotide at this position is a purine whereas in MS2, it is a pyrimidine.Keywords: bacteriophage coat protein; crystal structure; RNA hairpin; translational repressor; virus RNA bacteriophages are small viruses with a simple organization. These viruses have an icosahedral shell composed of 180 copies of coat protein and one copy of the maturation protein that encapsidate genomic RNA ,which is approximately 3,500 nucleotides in length. The single-stranded RNA genome also acts as mRNA, encoding four proteins: the viral coat protein, a maturation protein, a replicase subunit, and the lysis protein. These phages were first isolated from Escherichia coli, but later were also found in Caulobacter and Pseudomonas. To date, the coliphages have been the best studied and are classified into four groups based on serological and physicochemical properties. Groups I and I1 are quite similar, with MS2 and GA phages being the well-characterized members of these groups. Phages Q p and SP, members of Groups I11 and IV, respectively, are more divergent from Groups I and 11.

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OMITMAP: An electron density map suitable for the examination of errors in a macromolecular model

Cited by 133 publications

References 6 publications

Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme

Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme

Assessment of phase accuracy by cross validation: the free R value. Methods and applications

Crystal structure of the coat protein from the GA bacteriophage: Model of the unassembled dimer

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