Structure coordinates in PDB file
The atom numbered 1 in a PDB file is the most N-terminal atom visualized by the structure determination — the most N-terminal amino acid, the co-ordinates of which are presented.
If the X-ray diffraction (or whatever technique used) does resolve the first amino acid, then it will, in fact, be the first amino acid. The following is an arbitrary example from 4LI3 (chain X):
ATOM      1  N   MET X   1     100.329 111.822  35.431  1.00 66.81           N  
ATOM      2  CA  MET X   1     100.845 110.803  34.526  1.00 67.85           C  
ATOM      3  C   MET X   1     101.961 111.361  33.646  1.00 71.14           C  
ATOM      4  O   MET X   1     102.979 111.840  34.153  1.00 77.28           O  
ATOM      5  CB  MET X   1      99.722 110.256  33.648  1.00 61.70           C  
ATOM      6  CG  MET X   1      98.581 109.621  34.412  1.00 66.53           C  
ATOM      7  SD  MET X   1      97.327 108.947  33.300  1.00 82.23           S  
ATOM      8  CE  MET X   1      96.071 108.440  34.463  1.00 69.80           C  
ATOM      9  N   ALA X   2     101.754 111.288  32.331  1.00 67.01           N

If the X-ray diffraction does not resolve the first amino acid, or if the structure is of a fragment of the protein that does not contain the first amino acid, then the co-ordinates of the first amino acid are not listed in the file and ATOM 1 is from the most N-terminal amino acid. The following is an arbitrary example from 1BTE (chain A), starting at amino acid 7:
ATOM      1  N   GLU A   7      15.888  47.505  13.150  1.00 34.63           N
ATOM      2  CA  GLU A   7      14.455  47.789  12.947  1.00 33.53           C
ATOM      3  C   GLU A   7      13.538  46.900  13.794  1.00 29.91           C
ATOM      4  O   GLU A   7      12.342  46.832  13.476  1.00 30.54           O
ATOM      5  CB  GLU A   7      14.084  47.715  11.461  1.00 37.16           C
ATOM      6  CG  GLU A   7      14.284  46.356  10.821  1.00 41.38           C
ATOM      7  CD  GLU A   7      14.124  46.366   9.313  1.00 43.82           C
ATOM      8  OE1 GLU A   7      12.959  46.323   8.849  1.00 46.10           O
ATOM      9  OE2 GLU A   7      15.151  46.420   8.600  1.00 45.51           O

(Knowledge of the first amino acid is from nucleic acid sequencing.)