Brookhaven Data Bank

Now let us examine the relationships between handedness of Xs, Ca—Ca distance, and X2 values. Among the disulfides for which coordinates were available at 2 A resolution or better (Deisenhofer and Steigemann, 1975 Imoto et al., 1972 Wyckoff et al., 1970 Quiocho and Lipscomb, 1971 Saul et al., 1978 Epp et al., 1975 Huber et al., 1974 Chambers and Stroud, 1979 Hendrickson and Teeter, 1981 Brookhaven Data Bank, 1980 Feldmann, 1977), there are equal numbers with right-handed and left-handed xs- The average Ca—Ca distance across the left-handed ones is 6.1 A, exactly what was seen in the small-molecule structures, but for the right-handed ones the average Ca—Ca distance is 5.2 A. Clearly the two sets of disulfides as they occur in proteins cannot simply be mirror images of one another. 

Fig. 5.8. Three-dimensional structure of P. aeruginosa azurin. Coordinates from ref. [80] and Brookhaven Data Bank. Graphic representation by Molscript [66], The copper atom is indicated by the large sphere at the top, the disulphide group by the two smaller, lightly...

Figure 4.6. Monomer structure of the monocle chemotactic protein 1 (MCP-1). The structure was retrieved from the Brookhaven data bank (http // www.pdb.bnl.gov/) and displayed by Insight software (MolecularSimulations, San Diego, CA).

Fig. 13. Tertiary structure of plastocyanin from poplar. The two, four-stranded planes oppose each other and enclose the copper ion. From Ryden and Hunt 1993 [71] with permission. The coordinates for oxidized poplar pastocyanin originally determined by [22] were obtained from the Brookhaven Data Bank. The program MOLSCRIPT [79] was used for depiction...

Fig. 6. Structure of the Fc fragment of human IgG. ( ), Alpha carbon positions (o), approximate centres of carbohydrate hexose units. Coordinates were obtained from the Brookhaven Data Bank (after Dei-senhofer [23]). The pairing of Cn3 domains and the position of carbohydrate between C 2 domains is clearly seen in this view. The contact between carbohydrate chains is much more extensive in rabbit Fc. Note that the heavy chains are described only from residue 238 residues 225-238 do not show well-defined electron density.

For each set of loops, all examples were extracted from the Brookhaven Data Bank [7] and characterized according to loop length, 0, y/ conformation, sequence and structural superposition. The distribution of loop lengths (Figure 15.4) shows that nearly 70% have five or less residues. The loops that form structural families are indicated by shading in Figure 15.4 and summarized in Table 15.2. As expected, the families occur in the very short loops, where the number of possible conformations is small. These families are described in detail by Thornton and coworkers [22], and here we present just one family from each supersecondary group, as an example of the sorts of pattern observed. 

The simplest supersecondary 8-structural motif is formed by two sequential P strands. These can be in the same sheet, in which case they can either be antiparallel or parallel to one another (Figure 15.13a and 15.13b), or they can be in different sheets, forming an inter-sheet connection (Figure 15.13c). The pie chart in Figure 15.14 shows the fraction of sequential strand connections that are parallel, antiparallel and inter-sheet. The data were extracted automatically from a non-homologous data set of 90 protein structures in the Brookhaven Data Bank [7]. 

Table 15.3. Possible topologies of three-stranded P structural motifs and their frequencies in a set of 90 non-homologous proteins from the Brookhaven Data Bank...

Fig. 15.20. Classification of four-stranded Greek-key motifs based on their hydrogen-bonding patterns. The frequencies of occurrence in a non-homologous set of proteins from the Brookhaven Data Bank are shown for each class. The thin dotted lines in the (3,1) Greek keys represent strands behind the other P sheet the thick dotted lines represent strands in front of the P sheet. In the (2,2) Greek keys there are two strands in each of two sheets (above and below) the strands within each sheet are hydrogen bonded but the hydrogen bonds have been omitted for clarity...

Name of the entry code in the Brookhaven data bank.Number of observed unique reflections/number of parameters necessary to define the model. Neutral (dark) state. Charge separated state (light). 

Preparation of a Brookhaven Protein Data Bank (PDB)-formatted [10] file containing the coordinates and appropriate names of all atoms, including all polar and aromatic hydrogens. 

To find appropriate empirical pair potentials from the known protein structures in the Brookhaven Protein Data Bank, it is necessary to calculate densities for the distance distribution of Ga-atoms at given bond distance d and given residue assignments ai,a2- Up to a constant factor that is immaterial for subsequent structure determination by global optimization, the potentials then ciiiergo as the negative logarithm of the densities. Since... 

We tested our new potential by applying a local optimization procedure to the potential of some proteins, starting with the native structure as given in the Brookhaven Protein Data Bank, and observing how far the coordinates moved through local optimization. For a good potential, one expects the optimizer to be close to the native structure. As in Ulrich et al. [34], we measure the distance between optimizer B and native structure A by the distance matrix error... 

D.R. Stampf, C.E. Felser and J.L. Sussman, PDBBrowse - a graphics interface to the Brookhaven Protein Data Bank, Nature 374 (1995), 572-574. 

L.L. Walsh, Navigating the Brookhaven Protein Data Bank, Gabos Communication 10 (1994), 551-557. 

In 1971 the Protein Data Bank - PDB [146] (see Section 5.8 for a complete story and description) - was established at Brookhaven National Laboratories - BNL -as an archive for biological macromolccular cr7stal structures. This database moved in 1998 to the Research Collaboratory for Structural Bioinformatics -RCSB. A key component in the creation of such a public archive of information was the development of a method for effreient and uniform capture and curation of the data [147], The result of the effort was the PDB file format [53], which evolved over time through several different and non-uniform versions. Nevertheless, the PDB file format has become the standard representation for exchanging inacromolecular information derived from X-ray diffraction and NMR studies, primarily for proteins and nucleic acids. In 1998 the database was moved to the Research Collaboratory for Structural Bioinformatics - RCSB. 

HyperChem contains a database of amino and nucleic acid residues so you can quickly build polymers con laining these subunits. You can also read in structures in files from standard databases, such as the Brookhaven Protein Data Bank (see the HyperChem Reference Manual). 

PDB Databases Brookhaven Protein Data Bank Brookhaven National Laboratory... 

Fig. 3. Representation of the nine principal folds which recur in protein stmctures, where the codes of the representative proteins taken from the Brookhaven Protein Data Bank (PDB) (17) are given in parentheses (18) (1) globin (Ithb) (2) trefoil (lilb) (3) up—down (256b) (4) immunoglobulin folds...

The Brookhaven Protein Data Bank, PDB (http //www.pdb.bnl.gov), is the primary store of experimentally determined atomic coordinates of proteins. Each coordinate set has a unique identification code that can be... 

Molecule specifications can be entered by hand or be converted from the output of a graphics program. We ll perform a simple conversion here, converting the water molecule structure saved in Brookhaven Protein Data Bank (PDB) format. The file water. pdb in the quick subdirectory contains a PDB format structure for water. 

We ll look at a simple example of the latter method here, converting the water molecule structure saved in Brookhaven Protein Data Bank (PDB) format. 

All metric data for proteins are taken from the structures deposited in the Brookhaven Protein Data Bank. 

Fig. 7.23 Comparison of calculated and observed (x-ray ) mean N-C(a)-C bond angles for 37 proteins selected as described by Jiang et al. (1997,G). This reference is also the source of the values plotted, which are the region-average values, and . Regions of cb/ri-space and region numbering are explained in the lower graph. Experimental values (x-ray) were taken from the Brookhaven Protein Data Bank Chemistry Department, Building 555 Brookhaven National Laboratory, Box 5000, Upton N.Y. 11973-5000). The calculated values were obtained as described in the text.

R. Moschel, J. J. Stezowski, and D. E. Zacharias for many helpful discussions and collaborations. Most of the diagrams were drawn using the computer programs VIEW (141) and DOCK (142). Figure 21 was drawn with data obtained from the Protein Data Bank, Brookhaven. The work of the author was supported by grants CA-10925, CA-22780, CA-06927, RR-05539 from the National Institutes of Health, BC-242 from the American Cancer Society, and by an appropriation from the Commonwealth of Pennsylvania. 

Figure 6. Schematic representation of inositol monophosphate phosphatase (left) and inositol polyphosphate 1-phosphatase (right), showing the helical (green cylinders) and (3-sheet (yellow arrows) regions. The monophosphatase is complexed with lns(1)P (solid spheres) and Gd3+ (orange sphere) in the binding cleft and the polyphosphatase has two Mg2+ (lilac spheres) ions. (The coordinates were obtained from the Brookhaven Protein Data Bank).

Another major source are the amino acid sequences direcdy derived from protein sequencing. Thousands of such sequences have been detected by the SWISS-PROT curators in publications (or have been directly submitted by researchers to SWISS-PROT) and entered into the database. Protein sequences detected by the NCBI journal scan have also been included. For some proteins the Brookhaven Protein Data Bank (PDB) (Abola et al., 1996) is the only source for the sequence information. The PDB entries are checked regularly, and new SWISS-PROT entries were created whenever necessary. 

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