X-ray detection xray/facilities.html

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.

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

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.

PDB Protein Data Bank (PDB) –URL: –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

PDB Format HEADER TRANSFERASE (METHYLTRANSFERASE) 05-JAN-96 1VID TITLE CATECHOL O-METHYLTRANSFERASE HELIX 1 1 LYS 5 ASN HELIX 2 2 PRO 22 GLN HELIX 3 3 GLY 43 TYR HELIX 4 4 TYR 71 LEU HELIX 5 5 PRO 93 ALA HELIX 6 6 SER 119 TYR HELIX 7 7 LYS 144 LYS HELIX 8 8 PRO 177 GLY SHEET 1 A 7 PHE 189 TYR SHEET 2 A 7 VAL 204 TYR N ILE 211 O GLU 190 SHEET 3 A 7 VAL 165 ALA N ALA 168 O GLU 208 SHEET 4 A 7 MET 137 LEU 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 N THR 113 O LEU 86 ATOM 1 N THR N ATOM 2 CA THR C ATOM 3 C THR C ATOM 4 O THR O ATOM 5 CB THR C ATOM 6 OG1 THR O ATOM 7 CG2 THR C

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

B-factor Last value in the row –B-factor –a measurement for the atomic position –measured in Å Å 2 is about a RMS of  1 Å. ATOM 2 CA THR ATOM 3 C THR ATOM 4 O THR ATOM 5 CB THR ATOM 6 OG1 THR

Example 1crn ATOM 203 C TYR CRN 272 ATOM 204 O TYR CRN 273 ATOM 205 CB TYR CRN 274 ATOM 206 CG TYR CRN 275 ATOM 207 CD1 TYR CRN 276 ATOM 208 CD2 TYR CRN 277 ATOM 209 CE1 TYR CRN 278 ATOM 210 CE2 TYR CRN 279 ATOM 211 CZ TYR CRN 280 ATOM 212 OH TYR CRN 281 ATOM 213 N THR CRN 282 ATOM 214 CA THR CRN 283 Poor alignment caused by Bill Gates who doesn’t understand the Courier font.

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