Hi Jan, I do the same thing, but it would be nice if there was a consistent target. I noticed that the targets (and their sigmas) used by the PDB validation software don't fully coincide with the 'ideal' values from their own Chemical Component Dictionary. How are supposed to correct the restraint files if needed?
As for glycosidic linkages, there is no central repository for LINK targets at all in the PDB. It would be great if there were. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Jan Dohnalek > Sent: Monday, June 19, 2017 11:33 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] N-linked glycosylation check > > From a recent checks I did on one of our structures I have the strong feeling > that the library values behind Molprobity differ from the CCP4 library > (sugars) - in some cases seriously. > > In fact also behind wwPDB libs. > We then always check the library we refine against carefully and once happy > we just ignore any further warnings ... > > > Jan Dohnalek > > > > On Mon, Jun 19, 2017 at 10:54 AM, Chris Ulens <chris.ul...@kuleuven.be > <mailto:chris.ul...@kuleuven.be> > wrote: > > > Good morning, > I am looking to get feedback from others who have recently built and > refined bond lengths and angles of an N-linked glycosyl chain in Refmac. > I observed in Coot that the bond between O3 of BMA303 and C1 of > MAN304 does show while the bond between O6 of BMA303 and C1 of > MAN305 does not and I wonder why. > Molprobity issues warnings for bond length and angle outliers for the > entire chain. I have copied the relevant PDB lines below. > > Thank you for your help. > Best regards > Chris > > > > LINKR C1 NAG B 301 ND2 ASN B 108 > NAG-ASN > LINKR O4 NAG B 301 1.439 C1 NAG B 302 > BETA1-4 > LINKR O4 NAG B 302 1.439 C1 BMA B 303 > ALPHA1- > 4 > LINKR O3 BMA B 303 1.439 C1 MAN B 304 > BETA1- > 3 > LINKR O6 BMA B 303 1.439 C1 MAN B 305 > BETA1- > 6 > ATOM 2609 N ASN B 108 14.827 -15.743 -7.774 1.00 68.73 > N > ATOM 2610 CA ASN B 108 14.379 -16.001 -9.161 1.00 68.24 > C > ATOM 2611 CB ASN B 108 15.440 -16.789 -9.973 1.00 68.43 > C > ATOM 2612 CG ASN B 108 15.523 -18.271 -9.618 1.00 70.34 > C > ATOM 2613 OD1 ASN B 108 14.776 -18.790 -8.780 1.00 68.94 > O > ATOM 2614 ND2 ASN B 108 16.451 -18.966 -10.296 1.00 74.17 > N > ATOM 2615 C ASN B 108 12.982 -16.637 -9.178 1.00 68.93 > C > ATOM 2616 O ASN B 108 12.427 -16.943 -8.116 1.00 66.58 > O > HETATM 3393 C1 NAG B 301 16.707 -20.385 -10.157 1.00 77.65 > C > HETATM 3394 O5 NAG B 301 18.065 -20.635 -9.781 1.00 78.99 > O > HETATM 3395 C5 NAG B 301 18.330 -22.011 -9.454 1.00 80.39 > C > HETATM 3396 C6 NAG B 301 19.783 -22.145 -9.032 1.00 78.67 > C > HETATM 3397 O6 NAG B 301 20.614 -21.561 -10.039 1.00 78.50 > O > HETATM 3398 C4 NAG B 301 18.025 -22.927 -10.646 1.00 82.50 > C > HETATM 3399 O4 NAG B 301 18.039 -24.305 -10.255 1.00 85.12 > O > HETATM 3400 C3 NAG B 301 16.640 -22.661 -11.203 1.00 81.09 > C > HETATM 3401 O3 NAG B 301 16.488 -23.414 -12.412 1.00 81.20 > O > HETATM 3402 C2 NAG B 301 16.428 -21.169 -11.448 1.00 79.40 > C > HETATM 3403 N2 NAG B 301 15.066 -21.042 -11.942 1.00 79.12 > N > HETATM 3404 C7 NAG B 301 14.706 -20.379 -13.047 1.00 78.12 > C > HETATM 3405 C8 NAG B 301 13.243 -20.422 -13.354 1.00 78.57 > C > HETATM 3406 O7 NAG B 301 15.476 -19.768 -13.766 1.00 76.05 > O > HETATM 3407 C1 NAG B 302 19.037 -25.083 -10.947 1.00 87.76 > C > HETATM 3408 O5 NAG B 302 18.655 -25.448 -12.270 1.00 87.97 > O > HETATM 3409 C5 NAG B 302 19.667 -26.160 -12.982 1.00 89.21 > C > HETATM 3410 C6 NAG B 302 19.082 -26.481 -14.347 1.00 90.71 > C > HETATM 3411 O6 NAG B 302 19.210 -25.325 -15.180 1.00 95.46 > O > HETATM 3412 C4 NAG B 302 20.094 -27.444 -12.263 1.00 90.51 > C > HETATM 3413 O4 NAG B 302 21.315 -27.940 -12.855 1.00 93.27 > O > HETATM 3414 C3 NAG B 302 20.319 -27.252 -10.763 1.00 89.34 > C > HETATM 3415 O3 NAG B 302 20.255 -28.506 -10.070 1.00 88.92 > O > HETATM 3416 C2 NAG B 302 19.285 -26.337 -10.120 1.00 88.56 > C > HETATM 3417 N2 NAG B 302 19.762 -25.958 -8.795 1.00 88.35 > N > HETATM 3418 C7 NAG B 302 19.037 -26.050 -7.679 1.00 86.04 > C > HETATM 3419 C8 NAG B 302 19.763 -25.594 -6.443 1.00 86.11 > C > HETATM 3420 O7 NAG B 302 17.885 -26.464 -7.647 1.00 81.74 > O > HETATM 3421 C1 BMA B 303 21.616 -29.338 -12.590 1.00 96.54 > C > HETATM 3422 O5 BMA B 303 20.446 -30.174 -12.479 1.00 98.08 > O > HETATM 3423 C5 BMA B 303 20.540 -31.614 -12.489 1.00 99.62 > C > HETATM 3424 C6 BMA B 303 20.256 -32.208 -11.107 1.00100.50 > C > HETATM 3425 O6 BMA B 303 20.931 -31.469 -10.075 1.00100.33 > O > HETATM 3426 C4 BMA B 303 21.875 -32.103 -13.039 1.00 97.91 > C > HETATM 3427 O4 BMA B 303 21.772 -33.482 -13.431 1.00 95.77 > O > HETATM 3428 C3 BMA B 303 22.244 -31.206 -14.216 1.00 96.33 > C > HETATM 3429 O3 BMA B 303 23.273 -31.875 -14.962 1.00 94.34 > O > HETATM 3430 C2 BMA B 303 22.598 -29.814 -13.669 1.00 96.74 > C > HETATM 3431 O2 BMA B 303 23.919 -29.813 -13.104 1.00 97.73 > O > HETATM 3432 C1 MAN B 304 23.970 -31.058 -15.921 1.00 93.13 > C > HETATM 3433 O5 MAN B 304 23.200 -30.504 -16.999 1.00 92.48 > O > HETATM 3434 C5 MAN B 304 23.937 -29.452 -17.653 1.00 94.03 > C > HETATM 3435 C6 MAN B 304 23.073 -28.788 -18.726 1.00 93.77 > C > HETATM 3436 O6 MAN B 304 22.666 -29.744 -19.708 1.00 94.64 > O > HETATM 3437 C4 MAN B 304 25.272 -29.993 -18.201 1.00 93.08 > C > HETATM 3438 O4 MAN B 304 26.089 -28.900 -18.655 1.00 90.68 > O > HETATM 3439 C3 MAN B 304 26.034 -30.834 -17.160 1.00 92.23 > C > HETATM 3440 O3 MAN B 304 27.106 -31.570 -17.732 1.00 94.34 > O > HETATM 3441 C2 MAN B 304 25.134 -31.859 -16.488 1.00 92.52 > C > HETATM 3442 O2 MAN B 304 24.723 -32.907 -17.396 1.00 89.90 > O > HETATM 3443 C1 MAN B 305 21.455 -32.294 -9.018 1.00102.01 > C > HETATM 3444 O5 MAN B 305 21.325 -33.695 -8.914 1.00102.85 > O > HETATM 3445 C5 MAN B 305 22.576 -34.203 -9.377 1.00101.34 > C > HETATM 3446 C6 MAN B 305 22.439 -35.713 -9.516 1.00 99.57 > C > HETATM 3447 O6 MAN B 305 21.964 -36.012 -10.842 1.00 99.10 > O > HETATM 3448 C4 MAN B 305 23.716 -33.690 -8.465 1.00101.06 > C > HETATM 3449 O4 MAN B 305 24.981 -34.109 -8.996 1.00 99.42 > O > HETATM 3450 C3 MAN B 305 23.720 -32.144 -8.347 1.00101.15 > C > HETATM 3451 O3 MAN B 305 24.692 -31.689 -7.399 1.00100.86 > O > HETATM 3452 C2 MAN B 305 22.336 -31.620 -7.977 1.00101.26 > C > HETATM 3453 O2 MAN B 305 22.004 -32.090 -6.664 1.00 99.36 > O > TER 3454 MAN B 305 > TER 3455 MAN B 305 > > > > > > -- > > Jan Dohnalek, Ph.D > Institute of Biotechnology > > Academy of Sciences of the Czech Republic > > Biocev > > Prumyslova 595 > > 252 50 Vestec near Prague > > Czech Republic > > > Tel. +420 325 873 758
