1LYZ

Structural comparison between the unbound and bound states for various proteins using combinatorial extension Bound state a Unbound state b RMSD(Å) c Seq. PDB id Chain id PDB id Chain id ident... ty (%) Angiogenin 1a4y B 1un3 A 0.76 99.1 hGH 1a22 A 1hgu – d 2.68 68.4 Tissue factor e 1ahw C 1tfh A 1.39 100.0 Barnase 1brs A 1bnf A 1.12 98.1 Barstar 1brs D 1a19 A 0.44 98.9 BPTI 1cbw D 1bpt – d 0.39 98.2 Tissue factor e 1dan T 1tfh A 0.63 100.0 RNase inhibitor 1dfj I 2bnh – d 1.50 100.0 CD4 1gc1 C 1cdj A 1.09 100.0 Hen egg lysozyme e 1vfb C 1lyz – d 1.11 100.0 Trypsin 2ptc I 1bpt – d 0.36 98.2 Lysozyme e 3hfm Y 1lyz – d 0.67 100.0 a A protein is in the bound state.

Figure 2 Example of an Atlas page, in this case for PDB entry 1lyz .

Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3, Subset 3.1... RMSD(129) = 0.6481 4 hen egg-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 3, Subset 3.2 RMSD(164) = 0.24 8 mutant of phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 RMSD(124) = 0.1655 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5, Subset 5.1 RMSD(287)  = 0.8877 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse deoxyhemoglobin 2DHB 2201 287 2 5, Subset 5.2 RMSD(574)  = 1.501 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin (W37A) 1Y4F 4368 574 4 19 hemoglobin mutant (W37A) 1A01 4368 574 4 20 human hemoglobin (W37E) 1Y4P 4376 574 4 21 hemoglobin mutant (W37Y) 1A00 4382 574 4 22 human hemoglobin (W37Y) 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin (W37G) 1Y4G 4366 574 4 25 hemoglobin mutant (V1M) 1A0U 4386 574 4 26 hemoglobin mutant (V1M) 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 RMSD(585) = 2.3740 28 human serum albumin complexed with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 human serum albumin 1E78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 To quantify the similarity between the members of a class, for all sets, or subsets, i.e., for lysozyme and hemoglobins, the Root-Mean-Square Deviation (RMSD) has been calculated using the protein structure comparison service Fold at the European Bioinformatics Institute ( http://www.ebi.ac.uk/msd-srv/ssm ).

Structures were obtained by molecular substitution from published models and refined using REFMAC (Murshudov et al. , 2011 ▶ ) and ARP / wARP [Perrakis et al. , 2001 ▶ ; the starting m... dels were PDB entries 1lyz for lysozyme (Diamond, 1974 ▶ ), 4tln for thermolysin (Holmes & Matthews, 1981 ▶ ), 4i8g for trypsin (Liebschner et al. , 2013 ▶ ) and 3vca for stachydrine demethylase (Daughtry et al. , 2012 ▶ )].

For each X-ray diffraction data set, the 1LYZ structure was stripped of waters, refined with REFMAC , hydrated with ARP/wARP solvent, and the NAG was removed.

All six data sets supported a molecular-replacement solution using MOLREP (Vagin & Teplyakov, 1997 ▶ ) with a polyalanine search model ( 3rto and 1lyz , all residues changed to Ala) (D... amond, 1974 ▶ ).

Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3 4 chicken e... g-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 8 mutant phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse hemoglobin 2DHB 2201 287 2 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin 1Y4F 4368 574 4 19 hemoglobin mutant 1A01 4368 574 4 20 human hemoglobin 1Y4P 4376 574 4 21 hemoglobin mutant 1A00 4382 574 4 22 human hemoglobin 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin 1Y4G 4366 574 4 25 hemoglobin mutant 1A0U 4386 574 4 26 hemoglobin mutant 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 28 human serum albumin complex with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 serum albumin 1E_78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 Note: The proteins marked in bold are model proteins and those in italics have been also used for the analysis of statistical strength.

Structures were obtained by molecular substitution (using PDB entry 1lyz ; Diamond, 1974 ▶ ) and refined using REFMAC (Winn et al. , 2003 ▶ ) and ARP / wARP (Perrakis et al. , 2001 &#x... 25b6; ).

In the case of the tetragonal trapezoidal hen egg-white lysozyme (HEWL; PDB entry 1lyz ; Diamond, 1974 ▶ ), which contains eight molecules in the unit cell, this results in 46 992 poss... ble modes.

Structures were obtained by molecular substitution from published models and were refined using REFMAC (Winn et al. , 2003 ▶ ) and ARP / wARP (Perrakis et al. , 2001 ▶ ) (starting mode... s: lysozyme, PDB entry 1lyz ; thermolysin, 4tln ; stachydrine demethylase, 3vca ; photosystem II, 1fe1 ; Diamond, 1974 ▶ ; Holmes & Matthews, 1981 ▶ ; Daughtry et al. , 2012 ▶ ; Zouni et al. , 2001 ▶ ).