X-ray detection

www.chem.uky.edu/resources/ 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: 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

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

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 Å2. 80 Å2 is about a RMS of 1

Å.

ATOM 2 CA THR 1 16.967 12.784 4.338 1.00 10.80ATOM 3 C THR 1 15.685 12.755 5.133 1.00 9.19ATOM 4 O THR 1 15.268 13.825 5.594 1.00 9.85ATOM 5 CB THR 1 18.170 12.703 5.337 1.00 13.02ATOM 6 OG1 THR 1 19.334 12.829 4.463 1.00 15.06

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.

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