
PFRMAT ABF1
TARGET T0004
AUTHOR 5865-8356-4011 ANDRAS ASZODI, NIMR, a-aszodi@nimr.mrc.ac.uk
AUTHOR 5865-8356-4011 ROBIN E. J. MUNRO, NIMR, r-munro@nimr.mrc.ac.uk
AUTHOR 5865-8356-4011 WILLIAM R. TAYLOR, NIMR, w_taylor@nimr.mrc.ac.uk
REMARK
REMARK -------------- METHOD DESCRIPTION -------------------
REMARK
REMARK 1) MULTIPLE ALIGNMENT
REMARK The target sequence was aligned to the following homologous
REMARK sequences (SwissProt codes):
REMARK PNP_PHOLU,PNP_HAEIN,YABR_BACSU,RS1_MYCLE,RS1H_BACSU,
REMARK YHGF_ECOLI,RS1_ECOLI
REMARK using MULTAL [Taylor, W. R., J. Mol. Evol. 28:161 (1988)].
REMARK This step was done by R.E.J.M.
REMARK
REMARK 2) FOLD RECOGNITION
REMARK Threading was carried out using the program THREADER
REMARK [Jones, D. T. et al, Nature 358, 86-89.] The top 100 hits were
REMARK collected and the target plus the homologous sequences were
REMARK aligned against these using a new version of MSAP [Taylor, W. R.,
REMARK J. Mol. Biol., submitted]. Three hits were selected manually
REMARK from the MSAP output: chains 1LTSD,1HRHA and 2SNS.
REMARK These steps were done by R.E.J.M. and W.R.T.
REMARK
REMARK 3) FOLD GENERATION
REMARK The results of the MSAP alignments were submitted to DRAGON,
REMARK version 4.16.1 [Aszodi,A. et al., J.Mol.Biol. 251:308 (1995);
REMARK Aszodi,A. and Taylor,W.R., Folding&Design 1:325 (1996)] containing
REMARK the known structures and the target sequence only. 50 models
REMARK were generated for each of the three scaffold structures,
REMARK using C-alpha:C-alpha distances shorter than 10 A to guide
REMARK the folding process. Secondary structure assignments from the
REMARK scaffolds were also mapped onto the target at 30% probability.
REMARK This step was done by A.A.
REMARK
REMARK 4) MODEL BUILDING AND REFINEMENT
REMARK The 10 best-scoring DRAGON output structures were averaged for
REMARK each scaffold. These average structures (C-alpha atoms only)
REMARK constitute the datasets #1,2,3.
REMARK The missing atoms were added to the C-alpha average structures
REMARK and the resulting full-atom structures were minimised by
REMARK QUANTA Version 4.1/CHARMM 23.1. Initial geometry regularisation
REMARK was followed by an in vacuo simulated annealing at T=1000K
REMARK and a second MD run with an 8 A thick solvation layer at T=300 K.
REMARK These refined full-atom models are in the datasets #4,5,6.
REMARK The water molecules' positions are not given.
REMARK This step was done by A.A.
REMARK
REMARK ============== C-alpha TRACE (DRAGON output) =============
REMARK
REMARK Scaffold=1HRHA (Ribonuclease H-domain from HIV-1 reverse transcriptase)
REMARK C-alpha RMSD from the average:
REMARK     BEST RMS=1.1768e+00 A
REMARK     WORST RMS=2.3097e+00 A
REMARK     AVERAGE RMS=1.7126e+00 +/- 2.7258e-01 A
BEGDAT 3.1 2 1.0
ATOM      1  CA  ALA 0   1      -6.882  10.412   4.700  1.00  0.00
ATOM      2  CA  GLU 0   2      -5.925   9.607   2.240  1.00  0.00
ATOM      3  CA  ILE 0   3      -3.171   8.079   1.300  1.00  0.00
ATOM      4  CA  GLU 0   4      -1.131   6.377   2.733  1.00  0.00
ATOM      5  CA  VAL 0   5       1.453   4.968   3.004  1.00  0.00
ATOM      6  CA  GLY 0   6       4.616   4.661   2.451  1.00  0.00
ATOM      7  CA  ARG 0   7       6.632   4.497   4.853  1.00  0.00
ATOM      8  CA  VAL 0   8       8.405   3.397   7.044  1.00  0.00
ATOM      9  CA  TYR 0   9      11.204   4.027   8.191  1.00  0.00
ATOM     10  CA  THR 0  10      12.362   3.954   6.209  1.00  0.00
ATOM     11  CA  GLY 0  11      13.480   0.616   4.971  1.00  0.00
ATOM     12  CA  LYS 0  12      12.184  -1.089   5.925  1.00  0.00
ATOM     13  CA  VAL 0  13       9.490  -0.605   3.584  1.00  0.00
ATOM     14  CA  THR 0  14       8.098  -3.346   1.812  1.00  0.00
ATOM     15  CA  ARG 0  15       6.744  -5.730   4.580  1.00  0.00
ATOM     16  CA  ILE 0  16       5.459  -2.917   6.797  1.00  0.00
ATOM     17  CA  VAL 0  17       4.305  -0.825   3.307  1.00  0.00
ATOM     18  CA  ASP 0  18       1.404  -3.513   3.203  1.00  0.00
ATOM     19  CA  PHE 0  19       0.884  -2.876   7.213  1.00  0.00
ATOM     20  CA  GLY 0  20       0.479   1.084   6.142  1.00  0.00
ATOM     21  CA  ALA 0  21      -1.904  -0.461   3.111  1.00  0.00
ATOM     22  CA  PHE 0  22      -3.838  -2.655   6.031  1.00  0.00
ATOM     23  CA  VAL 0  23      -4.512   0.667   8.092  1.00  0.00
ATOM     24  CA  ALA 0  24      -5.453   2.737   4.839  1.00  0.00
ATOM     25  CA  ILE 0  25      -7.770  -0.075   3.364  1.00  0.00
ATOM     26  CA  GLY 0  26     -10.537  -0.006   5.409  1.00  0.00
ATOM     27  CA  GLY 0  27     -10.832   3.611   5.480  1.00  0.00
ATOM     28  CA  GLY 0  28     -12.053   5.488   3.494  1.00  0.00
ATOM     29  CA  LYS 0  29     -14.629   4.334   1.248  1.00  0.00
ATOM     30  CA  GLU 0  30     -14.361   5.976  -1.937  1.00  0.00
ATOM     31  CA  GLY 0  31     -11.412   7.375  -3.215  1.00  0.00
ATOM     32  CA  LEU 0  32      -8.501   6.324  -2.327  1.00  0.00
ATOM     33  CA  VAL 0  33      -6.198   4.384  -1.455  1.00  0.00
ATOM     34  CA  HIS 0  34      -3.120   4.526  -2.044  1.00  0.00
ATOM     35  CA  ILE 0  35      -0.248   3.196  -1.963  1.00  0.00
ATOM     36  CA  SER 0  36      -1.034  -0.168  -3.046  1.00  0.00
ATOM     37  CA  GLN 0  37       1.318  -1.292  -4.209  1.00  0.00
ATOM     38  CA  ILE 0  38       2.059  -4.394  -2.752  1.00  0.00
ATOM     39  CA  ALA 0  39      -1.764  -4.842  -3.028  1.00  0.00
ATOM     40  CA  ASP 0  40      -1.253  -5.629  -6.229  1.00  0.00
ATOM     41  CA  LYS 0  41       1.498  -7.942  -5.913  1.00  0.00
ATOM     42  CA  ARG 0  42       0.017  -9.307  -4.793  1.00  0.00
ATOM     43  CA  VAL 0  43      -2.183  -9.678  -2.960  1.00  0.00
ATOM     44  CA  GLU 0  44      -0.666 -12.916  -2.660  1.00  0.00
ATOM     45  CA  LYS 0  45       1.486 -13.968  -1.947  1.00  0.00
ATOM     46  CA  VAL 0  46       1.406 -14.225   1.309  1.00  0.00
ATOM     47  CA  THR 0  47       0.683 -13.999   4.164  1.00  0.00
ATOM     48  CA  ASP 0  48      -0.422 -10.367   4.659  1.00  0.00
ATOM     49  CA  TYR 0  49      -2.725 -10.858   2.514  1.00  0.00
ATOM     50  CA  LEU 0  50      -5.693 -13.002   2.352  1.00  0.00
ATOM     51  CA  GLN 0  51      -7.457 -10.117   4.955  1.00  0.00
ATOM     52  CA  MET 0  52      -5.717  -7.366   2.375  1.00  0.00
ATOM     53  CA  GLY 0  53      -7.534  -9.058  -0.779  1.00  0.00
ATOM     54  CA  GLN 0  54     -10.967  -9.473   1.395  1.00  0.00
ATOM     55  CA  GLU 0  55     -10.662  -5.518   2.365  1.00  0.00
ATOM     56  CA  VAL 0  56      -9.726  -4.712  -1.503  1.00  0.00
ATOM     57  CA  PRO 0  57     -13.430  -4.758  -2.675  1.00  0.00
ATOM     58  CA  VAL 0  58     -14.421  -1.381  -1.056  1.00  0.00
ATOM     59  CA  LYS 0  59     -15.496   0.678  -3.771  1.00  0.00
ATOM     60  CA  VAL 0  60     -14.435   1.003  -7.144  1.00  0.00
ATOM     61  CA  LEU 0  61     -11.582   3.156  -7.613  1.00  0.00
ATOM     62  CA  GLU 0  62      -8.840   2.104  -5.987  1.00  0.00
ATOM     63  CA  VAL 0  63      -5.820   1.079  -5.890  1.00  0.00
ATOM     64  CA  ASP 0  64      -2.876   2.097  -6.484  1.00  0.00
ATOM     65  CA  ARG 0  65      -0.490   3.816  -8.132  1.00  0.00
ATOM     66  CA  GLN 0  66      -1.657   7.058  -9.371  1.00  0.00
ATOM     67  CA  GLY 0  67      -2.742   9.113  -6.541  1.00  0.00
ATOM     68  CA  ARG 0  68       0.018  10.333  -4.515  1.00  0.00
ATOM     69  CA  ILE 0  69       2.924   9.543  -5.636  1.00  0.00
ATOM     70  CA  ARG 0  70       6.119   8.842  -6.236  1.00  0.00
ATOM     71  CA  LEU 0  71       7.544  11.211  -3.330  1.00  0.00
ATOM     72  CA  SER 0  72       6.135   8.690  -0.562  1.00  0.00
ATOM     73  CA  ILE 0  73       6.995   5.452  -2.770  1.00  0.00
ATOM     74  CA  LYS 0  74      10.513   6.904  -3.994  1.00  0.00
ATOM     75  CA  GLU 0  75      11.395   8.138  -0.295  1.00  0.00
ATOM     76  CA  ALA 0  76      10.090   4.737   1.341  1.00  0.00
ATOM     77  CA  THR 0  77      11.981   2.452  -0.925  1.00  0.00
ATOM     78  CA  GLU 0  78      14.302   2.232  -1.922  1.00  0.00
ATOM     79  CA  GLN 0  79      15.542   0.921   0.715  1.00  0.00
ATOM     80  CA  SER 0  80      15.472  -0.840   1.698  1.00  0.00
ATOM     81  CA  GLN 0  81      16.778  -2.572  -0.756  1.00  0.00
ATOM     82  CA  PRO 0  82      15.520  -3.094  -3.249  1.00  0.00
ATOM     83  CA  ALA 0  83      12.339  -2.261  -4.251  1.00  0.00
ATOM     84  CA  ALA 0  84      12.737  -2.020  -5.307  1.00  0.00
ENDDAT 3.1
END
