Atomic coordinate files

Once a crystal structure has been determined, the information is communicated in the form of an atomic coordinates file. In addition to a list of the atomic positions, the coordinates file contains other information that deserves an explanation and requires attention by the user. Some of the terms included in an atomic coordinates file are explained briefly. It is hoped that the information will provide the reader with insights to evaluate the quality of the structure, distinguish between its well-defined and flexible regions, and make sensible decisions in structural analysis. 

Figure 4.14. Conversion of 2D structure into 3D structure. The 2D structure file from ISIS draw (stanley.skc) is converted into the 3D structure with WebLab Viewer Lite. It should be noted that the atomic coordinate file does not contain ATOM columns with residue ID.

The common atomic coordinate files for 3D structure in biochemistry is PDB format. The pdb files of polysaccharides, proteins, and nucleic acids can be retrieved from the Protein Data Bank at RCSB (http //www.rcsb.org/pdb/). On the home page (Figure 4.15), enter PDB ID (check the box query by PDB id only ) or keywords (check the box match exact word ) and click Find a structure button. Alternatively, initiate search/retrieval by selecting SearchLite. On the query page, enter the keyword (e.g., the name of ligand or biomacromolecule) and click Search button. Select the desired entry from the list of hits to access Summary information of the selected molecule. From the Summary information, select Download/Display file and then PDB Text and PDB noncompression format to retrieve the pdb file. In order to display 3D structure online, choose View structure followed by selecting one of 3D display options. The display can be saved in. jpg or. gif image format. 

Figure 14.3. Display of 3D structure with Chem3D. Heptapeptide, STANLEY, is constructed by entering HSerThreAlaAsnLeuGluTyrOH into the replacement box (left side, under icons). Alternatively an ISIS Draw, stanldy.skc can be converted to stanley.cdx (ChemDraw) and then imported into Chem3D. The atomic coordinates file is saved as Stanley.pdb and can be edited for protein modeling. Note The file does not contain ATOM columns with residue ID.)...

TABLE 7.11 Reliability characteristics of atomic coordinate files... 

The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

Figure 2-114. Atomic coordinate data section of the analy2ed PD B file.

The angles ot, p, and x relate to the orientation of the dipole nionient vectors. The geonieti y of interaction between two bonds is given in Fig. 4-16, where r is the distance between the centers of the bonds. It is noteworthy that only the bond moments need be read in for the calculation because all geometr ic features (angles, etc.) can be calculated from the atomic coordinates. A default value of 1.0 for dielectric constant of the medium would normally be expected for calculating str uctures of isolated molecules in a vacuum, but the actual default value has been increased 1.5 to account for some intramolecular dipole moment interaction. A dielectric constant other than the default value can be entered for calculations in which the presence of solvent molecules is assumed, but it is not a simple matter to know what the effective dipole moment of the solvent molecules actually is in the immediate vicinity of the solute molecule. It is probably wrong to assume that the effective dipole moment is the same as it is in the bulk pure solvent. The molecular dipole moment (File 4-3) is the vector sum of the individual dipole moments within the molecule. 

A diva It MM3 wilh Ihe cumrnand mm3. Answer questions file etheiie.mm3, parameter file Enter (default) line number 1, option 2. The defaull parameter sel is Ihe MM3 parameler sel don t ehange il. The line number starts Ihe system reading on the first line of your input file, and option 2 is the block diagonal followed by full matrix minimi7 ation mentioned at the end of the section on the Hessian matrix. You will see intermediate atomic coordinates as the system minimises the geometry, followed by a final steiic eireigy, Kird with 0, output Enter, cooidinates Enter,... 

First, it is not possible to determine hydrogen atom positions by X-ray crystallography. Thus the coordinates for the many hydrogen atoms in the molecule are missing from X-ray coordinate files. These coordinates must be added to the initial structure before the simulation is started. Several algorithms are available for ensuring reasonable placement of hydrogens. 

Unlike the native integration of DIVCON with the sander module in AMBER, the integration of CNS was done at the file system level. For every step of hybrid minimization, CNS, after receiving atomic coordinates from sander, calculates and outputs the forces as the gradient of Ex-ray in Eq. (13-11), which is then read by sander. Sander combines the forces from Ex-ray and Eqm/mm potential and updates the coordinates accordingly. This process proceeds until the R and free R factors converge, which usually takes a few hundreds of steps. 

Fig. 8 Proposed model for gramicidin S in a membrane according to the orientational constraints obtained from and N-NMR. The upright backbone alignment (r 80°) and slant of the /3-sheets (p -45°) are compatible with the formation of an oligomeric /3-barrel that is stabilized by hydrogen bonds (dotted lines). A The oligomer is depicted sideways from within the lipid bilayer interior (showing only backbone atoms for clarity, but with hydrophobic side chains added to one of the monomers). Atomic coordinates of GS were taken from a monomeric structure [4], and the two DMPC lipid molecules are drawn to scale (from a molecular dynamics simulation coordinate file). The bilayer cross-section is coloured yellow in its hydrophobic core, red in the amphiphilic regions, and light blue near the aqueous surface. B Illustrates a top view of the putative pore, although the number of monomers remains speculative...

The first task of chemoinformatics is to transform chemical knowledge, such as molecular structures and chemical reactions, into computer-legible digital information. The digital representations of chemical information are the foundation for all chemoin-formatic manipulations in computer. There are many file formats for molecular information to be imported into and exported from computer. Some formats contain more information than others. Usually, intended applications will dictate which format is more suitable. For example, in a quantum chemistry calculation the molecular input file usually includes atomic symbols with three-dimensional (3D) atomic coordinates as the atomic positions, while a molecular dynamics simulation needs, in addition, atom types, bond status, and other relevant information for defining a force field. 

ProSa reads all it needs to know about a protein from a file in PDB format. A detailed description of this standard format is given at the RCSB website [2]. Of all record types within a PDB file, only the ATOM records are used by ProSa. They contain both the amino acid sequence of a certain protein chain and the atomic coordinates (example PDB files come with the ProSa distribution). If a PDB file contains more than one chain, only one is read. The first chain is read by default, other chains can be specified by providing the respective chain identifier. All molecules other than polypeptides are ignored. For energy calculations, ProSa takes into account C° and atoms. Care has to be taken when dealing with residue... 

Figure 10.1 -NMR spectrum of thioredoxin, reducedform. Labels show chemical-shift values typical of various hydrogen types in protein chains having random coil conformation. Some signals lie outside these ranges because of specific interactions not present in random coils. Atom labels are as found in PDB coordinate files. Spectrum generously provided by Professor John M. Louis.

Editing requires knowledge of how atoms are named in the coordinate file, which is often, but not always, the same as PDB atom labels (Chapter 7, Section VIII). Thus viewers can produce an alpha-carbon-only model by Limiting... 

Plate 1 Stereo photograph of Zif268/DNA complex (see N. P. Pavletich and and C. O. Pabo, Science 252, 809, 1991). (For discussion, see Chapter l. )NOTE Atomic coordinates for preparing this display were obtained from the Protein Data Bank (PDB), which is described in Chapter 7. The PDB file code is lzaa. To expedite your access to all models shown in this book, I provide file codes in this format PDB lzaa. Image created by Swiss-PdbViewer, rendered by POV-Ray. To obtain these programs, see the CMCC Reader s Page. 

The second step performs the GRID calculation with a given probe on the three subunit models. In order to make the application of Boolean operations with the map files as easy as possible, the matrix dimension of the GRID box is exactly maintained as in the largest model, i.e. that with a+fi subunits, maintaining, for both subunits, the original complex atom coordinates. The three maps obtained are named A, B and C, respectively (Fig. 7.1). 

Each set of coordinates deposited with the PDB becomes a separate entry. Each entry is associated with an accession PDB code with a unique set of four alphanumeric characters. PDB and its mirror sites offer a text search engine that uses an index of all the textual information in each PDB record (e.g., PDB ID) an example of such an index is 1LYZ for hen s egg-white lysozyme. The first character is a version number. An identifier beginning with the number 0 signifies that the entry is purely bibliographic. The pdb file is a text file with an explanatory header followed by a set of atomic coordinates. The atomic coordinates are subjected to a set of standard stereochemical checks and are translated into a standard entry format for example, Figure 4.10 shows partial coordinate file for ILYZ.pdb or pdblLYZ.ent. 

Figure 4.10. PDB file (partial) for 3D structure of hen s egg-white lysozyme (ILYZ.pdb). The abbreviated file shows partial atomic coordinates for residues 34-36. Informational lines such as AUTHOR (contributing authors of the 3D structure), REVDAT, JRNL (primary bibliographic citation), REMARK (other references, corrections, refinements, resolution and missing residues in the structure), SEQRES (amino acid sequence), FTNOTE (list of possible hydrogen bonds), HELIX (initial and final residues of a-helices), SHEET (initial and final residues of / -sheets), TURN (initial and final residues of turns, types of turns), and SSBOND (disulfide linkages) are deleted here for brevity. Atomic coordinates for amino acid residues are listed sequentially on ATOM lines. The following HETATM lines list atomic coordinates of water and/or ligand molecules.

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