1. X-ray detection www.chem.uky.edu/resources/ xray/facilities.html

2. How can we solve structures X – ray detection. Normally the best. NMR. Not very precise. Looks like > 3 Å X-ray structures. Only small proteins (80 AA). Electron microscopy (> 7 Å) not useful for models and only the shape is seen, no details. Other spectroscopic methods sometimes are useful for indirect information, or very local information. E.g. EXAFS can give very detailed information about metal contacts.

6. Problems with PDB files The watermolecules often are just guessed, because they are difficult to see. C, N, and O cannot be distinguished. Hard to distinguish ion from water from alternate structure of amino acid side chain. Resolution > 1 Å Difficult on big proteins > 200 AA

7. Discussion Advantage: Better than everything else Because of the water molecules in the crystal there is a good congruence to the structure in the water surrounding Disadvantage: Difficulties in fabrication the crystals, specially membrane crystals are very difficulty to make.

8. PDB Protein Data Bank (PDB) –URL: http://www.rcsb.org/pdb/ –All coordinates of the proteins are collected there –Files are structured and formatted so easy to search –Contains all structures from X-ray and NMR –Older than the most databanks –Because it is historic it is very unflexible

14. PDB Format HEADER TRANSFERASE (METHYLTRANSFERASE) 05-JAN-96 1VID TITLE CATECHOL O-METHYLTRANSFERASE HELIX 1 1 LYS 5 ASN 16 1 12 HELIX 2 2 PRO 22 GLN 35 1 14 HELIX 3 3 GLY 43 TYR 57 1 15 HELIX 4 4 TYR 71 LEU 79 1 9 HELIX 5 5 PRO 93 ALA 106 1 14 HELIX 6 6 SER 119 TYR 130 1 12 HELIX 7 7 LYS 144 LYS 156 5 13 HELIX 8 8 PRO 177 GLY 185 1 9 SHEET 1 A 7 PHE 189 TYR 197 0 SHEET 2 A 7 VAL 204 TYR 212 -1 N ILE 211 O GLU 190 SHEET 3 A 7 VAL 165 ALA 168 -1 N ALA 168 O GLU 208 SHEET 4 A 7 MET 137 LEU 140 1 N VAL 138 O VAL 165 SHEET 5 A 7 LEU 61 LEU 65 1 N LEU 63 O MET 137 SHEET 6 A 7 ARG 85 GLU 90 1 N ARG 85 O VAL 62 SHEET 7 A 7 VAL 112 ASN 116 1 N THR 113 O LEU 86 ATOM 1 N THR 4 -32.796 52.984 34.270 1.00 25.07 N ATOM 2 CA THR 4 -32.168 53.250 35.602 1.00 25.39 C ATOM 3 C THR 4 -32.658 54.592 36.116 1.00 24.95 C ATOM 4 O THR 4 -33.177 55.399 35.337 1.00 25.40 O ATOM 5 CB THR 4 -30.631 53.322 35.498 1.00 26.05 C ATOM 6 OG1 THR 4 -30.256 54.471 34.725 1.00 26.33 O ATOM 7 CG2 THR 4 -30.077 52.059 34.847 1.00 26.84 C

15. B - factor The PDB databank gives also the B-factor Important for modelling Gives information about how precise the residue is located. B >= 100 means the atom exists but cannot be seen; B >=60 means atomic position is doubtful

16. B-factor Last value in the row –B-factor –a measurement for the atomic position –measured in Å 2. 80 Å 2 is about a RMS of  1 Å. ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80 ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19 ATOM 4 O THR 1 15.268 13.825 5.594 1.00 9.85 ATOM 5 CB THR 1 18.170 12.703 5.337 1.00 13.02 ATOM 6 OG1 THR 1 19.334 12.829 4.463 1.00 15.06

17. Example 1crn ATOM 203 C TYR 29 1.125 11.125 7.815 1.00 4.92 1CRN 272 ATOM 204 O TYR 29.286 10.632 8.545 1.00 7.13 1CRN 273 ATOM 205 CB TYR 29.755 11.229 5.322 1.00 9.66 1CRN 274 ATOM 206 CG TYR 29 -.203 10.044 5.354 1.00 11.56 1CRN 275 ATOM 207 CD1 TYR 29 -1.547 10.337 5.645 1.00 12.85 1CRN 276 ATOM 208 CD2 TYR 29.193 8.750 5.100 1.00 14.44 1CRN 277 ATOM 209 CE1 TYR 29 -2.496 9.329 5.673 1.00 16.61 1CRN 278 ATOM 210 CE2 TYR 29 -.801 7.705 5.156 1.00 17.11 1CRN 279 ATOM 211 CZ TYR 29 -2.079 8.031 5.430 1.00 19.99 1CRN 280 ATOM 212 OH TYR 29 -3.097 7.057 5.458 1.00 28.98 1CRN 281 ATOM 213 N THR 30 2.470 10.984 7.995 1.00 5.31 1CRN 282 ATOM 214 CA THR 30 2.986 9.994 8.950 1.00 5.70 1CRN 283 Poor alignment caused by Bill Gates who doesn’t understand the Courier font.

18. Examples 1ycq, 2,3 Ångstrom resolution, very bad 1chc: no resolution, very suspicious 1rdb, 1,9 Angstroem, better but B-values are high 2frt, is a model 1frt, 4,5 Angstroem resolution, no discussion