data_2JXG

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  2JXG
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   nmr
#
_pdbx_vrpt_summary.entry_id                    2JXG
_pdbx_vrpt_summary.PDB_deposition_date         2007-11-19
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2022-03-16
_pdbx_vrpt_summary.report_creation_date        2022-08-20:13:43
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,coreclust,chemicalshifts,percentiles,writepdf,writexml,writecif
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
_pdbx_vrpt_entity.id           1
_pdbx_vrpt_entity.type         polymer
_pdbx_vrpt_entity.description  "Proline dehydrogenase"
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  A  0.98  1.04  370  500  
2  1  1  B  B  0.98  1.04  370  500  
#
_pdbx_vrpt_summary_geometry.ordinal                                    1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers_full_length  2.33
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers_full_length       20.51
_pdbx_vrpt_summary_geometry.clashscore_full_length                     34.39
_pdbx_vrpt_summary_geometry.num_H_reduce                               755
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                             740
_pdbx_vrpt_summary_geometry.bonds_RMSZ                                 1.04
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                            1000
_pdbx_vrpt_summary_geometry.angles_RMSZ                                0.98
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  MET  A   1  .  ?        1  
 2  1  1  A   2  ALA  A   2  .  ?        1  
 3  1  1  A   3  THR  A   3  .  ?        1  
 4  1  1  A   4  THR  A   4  .  ?        1  
 5  1  1  A   5  THR  A   5  .  ?        ?  
 6  1  1  A   6  LEU  A   6  .  ?        1  
 7  1  1  A   7  GLY  A   7  .  ?        ?  
 8  1  1  A   8  VAL  A   8  .  ?        2  
 9  1  1  A   9  LYS  A   9  .  ?        4  
10  1  1  A  10  LEU  A  10  .  ?        2  
11  1  1  A  11  ASP  A  11  .  ?        3  
12  1  1  A  12  ASP  A  12  .  ?        ?  
13  1  1  A  13  PRO  A  13  .  ?        ?  
14  1  1  A  14  THR  A  14  .  ?        ?  
15  1  1  A  15  ARG  A  15  .  ?        ?  
16  1  1  A  16  GLU  A  16  .  ?        ?  
17  1  1  A  17  ARG  A  17  .  ?        ?  
18  1  1  A  18  LEU  A  18  .  ?        ?  
19  1  1  A  19  LYS  A  19  .  ?        ?  
20  1  1  A  20  ALA  A  20  .  ?        ?  
21  1  1  A  21  ALA  A  21  .  ?        ?  
22  1  1  A  22  ALA  A  22  .  ?        1  
23  1  1  A  23  GLN  A  23  .  ?        ?  
24  1  1  A  24  SER  A  24  .  ?        ?  
25  1  1  A  25  ILE  A  25  .  ?        1  
26  1  1  A  26  ASP  A  26  .  ?        2  
27  1  1  A  27  ARG  A  27  .  ?        4  
28  1  1  A  28  THR  A  28  .  ?        1  
29  1  1  A  29  PRO  A  29  .  ?        ?  
30  1  1  A  30  HIS  A  30  .  ?        3  
31  1  1  A  31  TRP  A  31  .  ?        4  
32  1  1  A  32  LEU  A  32  .  ?        7  
33  1  1  A  33  ILE  A  33  .  ?        ?  
34  1  1  A  34  LYS  A  34  .  ?        ?  
35  1  1  A  35  GLN  A  35  .  ?        2  
36  1  1  A  36  ALA  A  36  .  ?        ?  
37  1  1  A  37  ILE  A  37  .  ?        1  
38  1  1  A  38  PHE  A  38  .  ?        3  
39  1  1  A  39  ASN  A  39  .  ?        2  
40  1  1  A  40  TYR  A  40  .  ?        3  
41  1  1  A  41  LEU  A  41  .  ?        ?  
42  1  1  A  42  GLU  A  42  .  ?        ?  
43  1  1  A  43  LYS  A  43  .  ?        ?  
44  1  1  A  44  LEU  A  44  .  ?        3  
45  1  1  A  45  GLU  A  45  .  ?        ?  
46  1  1  B   1  MET  B  46  .  ?        1  
47  1  1  B   2  ALA  B  47  .  ?        1  
48  1  1  B   3  THR  B  48  .  ?        1  
49  1  1  B   4  THR  B  49  .  ?        1  
50  1  1  B   5  THR  B  50  .  ?        ?  
51  1  1  B   6  LEU  B  51  .  ?        ?  
52  1  1  B   7  GLY  B  52  .  ?        ?  
53  1  1  B   8  VAL  B  53  .  ?        2  
54  1  1  B   9  LYS  B  54  .  ?        4  
55  1  1  B  10  LEU  B  55  .  ?        2  
56  1  1  B  11  ASP  B  56  .  ?        1  
57  1  1  B  12  ASP  B  57  .  ?        ?  
58  1  1  B  13  PRO  B  58  .  ?        ?  
59  1  1  B  14  THR  B  59  .  ?        ?  
60  1  1  B  15  ARG  B  60  .  ?        1  
61  1  1  B  16  GLU  B  61  .  ?        ?  
62  1  1  B  17  ARG  B  62  .  ?        ?  
63  1  1  B  18  LEU  B  63  .  ?        ?  
64  1  1  B  19  LYS  B  64  .  ?        ?  
65  1  1  B  20  ALA  B  65  .  ?        ?  
66  1  1  B  21  ALA  B  66  .  ?        ?  
67  1  1  B  22  ALA  B  67  .  ?        1  
68  1  1  B  23  GLN  B  68  .  ?        ?  
69  1  1  B  24  SER  B  69  .  ?        ?  
70  1  1  B  25  ILE  B  70  .  ?        ?  
71  1  1  B  26  ASP  B  71  .  ?        1  
72  1  1  B  27  ARG  B  72  .  ?        5  
73  1  1  B  28  THR  B  73  .  ?        1  
74  1  1  B  29  PRO  B  74  .  ?        ?  
75  1  1  B  30  HIS  B  75  .  ?        3  
76  1  1  B  31  TRP  B  76  .  ?        5  
77  1  1  B  32  LEU  B  77  .  ?        7  
78  1  1  B  33  ILE  B  78  .  ?        ?  
79  1  1  B  34  LYS  B  79  .  ?        ?  
80  1  1  B  35  GLN  B  80  .  ?        1  
81  1  1  B  36  ALA  B  81  .  ?        ?  
82  1  1  B  37  ILE  B  82  .  ?        1  
83  1  1  B  38  PHE  B  83  .  ?        3  
84  1  1  B  39  ASN  B  84  .  ?        1  
85  1  1  B  40  TYR  B  85  .  ?        3  
86  1  1  B  41  LEU  B  86  .  ?        ?  
87  1  1  B  42  GLU  B  87  .  ?        ?  
88  1  1  B  43  LYS  B  88  .  ?        ?  
89  1  1  B  44  LEU  B  89  .  ?        3  
90  1  1  B  45  GLU  B  90  .  ?        ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
 1   1  mtm           ?       ?  ?        11   8  0.82  10  1.04  molprobity  
 2   2  ?         -65.2    60.6  OUTLIER   5   5  1.17   7  0.55  molprobity  
 3   3  p         -80.8    99.8  Favored   7   7  0.77  10  0.91  molprobity  
 4   4  m         -86.8   139.4  Favored   7   7  0.80  10  1.11  molprobity  
 5   5  OUTLIER   -91.0   112.3  Favored   7   7  0.68  10  1.12  molprobity  
 6   6  mt       -113.0   155.9  Favored  11   8  1.04  11  1.40  molprobity  
 7   7  ?         -74.3   131.1  Favored   3   4  1.38   5  1.05  molprobity  
 8   8  OUTLIER   -95.5   176.8  Allowed   9   7  1.09  10  0.76  molprobity  
 9   9  mttm     -124.6    76.1  Allowed  13   9  0.87  11  0.90  molprobity  
10  10  mt       -112.9   150.2  Favored  11   8  0.90  11  0.93  molprobity  
11  11  OUTLIER  -105.7   149.2  Favored   4   8  1.08  11  0.86  molprobity  
12  12  OUTLIER   -51.1   -60.8  Favored   4   8  1.01  12  0.75  molprobity  
13  13  Cg_exo    -42.8   -52.4  Favored   7   8  0.65  11  0.64  molprobity  
14  14  m         -64.0   -42.8  Favored   7   7  0.97  10  0.67  molprobity  
15  15  ttt85     -55.9   -38.5  Favored  13  11  1.35  14  1.12  molprobity  
16  16  mm-40     -65.6   -38.7  Favored   6   9  1.70  12  0.93  molprobity  
17  17  tmt_?     -64.9   -30.6  Favored  13  11  1.13  14  0.95  molprobity  
18  18  mp        -62.0   -35.6  Favored  11   8  0.90  11  0.96  molprobity  
19  19  OUTLIER   -52.7   -38.7  Favored  13   9  0.82  11  0.82  molprobity  
20  20  ?         -61.4   -40.2  Favored   5   5  1.08   7  0.86  molprobity  
21  21  ?         -63.6   -40.8  Favored   5   5  0.82   7  0.74  molprobity  
22  22  ?         -65.2   -34.6  Favored   5   5  1.12   7  0.51  molprobity  
23  23  mm-40     -63.7   -30.2  Favored   8   9  0.87  12  0.87  molprobity  
24  24  t         -58.1   -38.5  Favored   5   6  0.77   8  0.51  molprobity  
25  25  tt       -108.5   -14.4  Favored  11   8  0.98  11  0.79  molprobity  
26  26  t70        76.4    47.5  Allowed   4   8  0.91  11  0.66  molprobity  
27  27  mtt-85   -119.0  -177.2  Favored  13  11  1.30  14  1.10  molprobity  
28  28  OUTLIER   -77.5   140.7  Favored   7   7  0.86  11  1.13  molprobity  
29  29  Cg_exo    -46.8   -64.4  Allowed   7   8  1.13  11  0.91  molprobity  
30  30  t-160     -49.5   -51.7  Favored   7  11  1.11  15  0.89  molprobity  
31  31  t-105     -57.7   -34.4  Favored  10  16  1.04  23  1.73  molprobity  
32  32  tm?       -63.7   -42.2  Favored  11   8  0.94  11  0.81  molprobity  
33  33  mt        -50.6   -42.2  Favored  11   8  0.76  11  1.15  molprobity  
34  34  OUTLIER   -61.6   -41.8  Favored  13   9  0.97  11  1.22  molprobity  
35  35  mt-30     -65.7   -52.4  Favored   8   9  0.95  12  0.92  molprobity  
36  36  ?         -48.9   -31.9  Favored   5   5  0.99   7  0.65  molprobity  
37  37  tp        -91.8   -53.4  Favored  11   8  0.92  11  0.84  molprobity  
38  38  OUTLIER   -74.6   -45.7  Favored   9  12  1.12  16  0.78  molprobity  
39  39  t-20      -59.6   -34.1  Favored   6   8  0.92  11  0.88  molprobity  
40  40  t80       -59.7   -34.9  Favored   9  13  0.86  18  1.18  molprobity  
41  41  mt        -69.6   -44.7  Favored  11   8  0.86  11  0.89  molprobity  
42  42  tt0       -63.6   -30.6  Favored   6   9  1.60  12  0.91  molprobity  
43  43  mttp      -67.2   -65.6  Allowed  13   9  0.79  11  0.81  molprobity  
44  44  pp        -75.1     2.2  Favored  11   8  1.11  11  1.08  molprobity  
45  45  tp10          ?       ?  ?         6   8  1.54   9  0.97  molprobity  
46  46  mtm           ?       ?  ?         8   8  0.82  10  1.03  molprobity  
47  47  ?         -65.1    60.6  OUTLIER   5   5  1.19   7  0.56  molprobity  
48  48  p         -80.8    99.7  Favored   7   7  0.79  10  0.91  molprobity  
49  49  m         -86.6   139.0  Favored   7   7  0.82  10  1.11  molprobity  
50  50  OUTLIER   -90.7   112.3  Favored   7   7  0.68  10  1.10  molprobity  
51  51  mt       -112.9   155.6  Favored  11   8  1.03  11  1.42  molprobity  
52  52  ?         -74.2   131.2  Favored   3   4  1.37   5  1.08  molprobity  
53  53  OUTLIER   -95.5   176.6  Allowed   9   7  1.09  10  0.76  molprobity  
54  54  mttm     -124.2    76.6  Allowed  13   9  0.86  11  0.91  molprobity  
55  55  mt       -113.5   149.7  Favored  11   8  0.90  11  0.90  molprobity  
56  56  OUTLIER  -105.2   148.5  Favored   4   8  1.09  11  0.85  molprobity  
57  57  OUTLIER   -51.0   -61.2  Favored   4   8  0.99  12  0.74  molprobity  
58  58  Cg_exo    -42.5   -52.4  Favored   7   8  0.65  11  0.66  molprobity  
59  59  m         -64.2   -43.3  Favored   7   7  0.91  10  0.68  molprobity  
60  60  ttt85     -55.8   -37.9  Favored  13  11  1.35  14  1.11  molprobity  
61  61  mm-40     -65.4   -38.3  Favored   6   9  1.69  12  0.94  molprobity  
62  62  tmt_?     -64.6   -32.2  Favored  13  11  1.11  14  0.99  molprobity  
63  63  mp        -60.9   -35.6  Favored  11   8  0.90  11  0.95  molprobity  
64  64  OUTLIER   -53.0   -38.6  Favored  13   9  0.81  11  0.83  molprobity  
65  65  ?         -61.5   -39.8  Favored   5   5  1.08   7  0.87  molprobity  
66  66  ?         -63.7   -40.9  Favored   5   5  0.82   7  0.75  molprobity  
67  67  ?         -65.2   -34.2  Favored   5   5  1.15   7  0.53  molprobity  
68  68  mm-40     -63.8   -30.4  Favored   8   9  0.86  12  0.89  molprobity  
69  69  t         -58.6   -38.1  Favored   5   6  0.80   8  0.49  molprobity  
70  70  tt       -110.0    -9.3  Favored  11   8  0.96  11  0.75  molprobity  
71  71  t70        71.0    50.3  Allowed   4   8  0.92  11  0.67  molprobity  
72  72  mtt-85   -121.0  -177.5  Favored  13  11  1.34  14  1.03  molprobity  
73  73  OUTLIER   -77.4   140.1  Favored   7   7  0.86  11  1.10  molprobity  
74  74  Cg_exo    -47.0   -63.7  Allowed   7   8  1.13  11  0.93  molprobity  
75  75  t-160     -50.0   -52.5  Favored   7  11  1.13  15  0.90  molprobity  
76  76  t-105     -57.0   -34.4  Favored  10  16  1.07  23  1.76  molprobity  
77  77  tm?       -63.6   -42.2  Favored  11   8  0.94  11  0.81  molprobity  
78  78  mt        -50.3   -42.4  Favored  11   8  0.75  11  1.16  molprobity  
79  79  OUTLIER   -61.6   -42.0  Favored  13   9  0.97  11  1.20  molprobity  
80  80  mt-30     -65.5   -51.8  Favored   8   9  0.97  12  0.94  molprobity  
81  81  ?         -49.0   -32.0  Favored   5   5  0.97   7  0.65  molprobity  
82  82  tp        -92.2   -53.0  Favored  11   8  0.93  11  0.82  molprobity  
83  83  OUTLIER   -74.2   -46.2  Favored   9  12  1.12  16  0.76  molprobity  
84  84  t-20      -60.0   -33.9  Favored   6   8  0.92  11  0.88  molprobity  
85  85  t80       -59.7   -34.9  Favored   9  13  0.88  18  1.19  molprobity  
86  86  mt        -70.2   -44.3  Favored  11   8  0.85  11  0.88  molprobity  
87  87  tt0       -63.4   -29.9  Favored   6   9  1.61  12  0.91  molprobity  
88  88  mttp      -67.8   -65.8  Allowed  13   9  0.78  11  0.82  molprobity  
89  89  pp        -75.2     4.6  Favored  11   8  1.09  11  1.09  molprobity  
90  90  tp10          ?       ?  ?         6   8  1.56   9  0.95  molprobity  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
  1   1  O      1  0.50  2.42  
  2   2  O      2  0.43  2.37  
  3   3  N      1  0.50  2.42  
  4   4  N      3  0.53  2.42  
  5   6  CD1    4  0.40  2.84  
  6   8  HG11   5  0.69  1.62  
  7   8  HG13   6  0.43  2.28  
  8   9  HZ3    7  0.65  2.09  
  9   9  NZ     8  0.60  2.70  
 10   9  NZ     9  0.60  2.50  
 11   9  N      6  0.43  2.28  
 12  10  HD12   5  0.69  1.62  
 13  10  O     10  0.50  2.41  
 14  11  OD1   11  0.42  2.37  
 15  11  OD1   12  0.40  2.55  
 16  11  N     12  0.40  2.55  
 17  22  O     13  0.53  2.40  
 18  25  O     14  0.44  2.64  
 19  26  N     13  0.53  2.40  
 20  26  CB    14  0.44  2.64  
 21  27  NH1   15  0.62  2.46  
 22  27  NH1   16  0.48  2.82  
 23  27  NH1   17  0.45  2.85  
 24  27  CZ    18  0.50  2.75  
 25  28  O     19  0.42  2.51  
 26  30  CD2   20  0.62  2.13  
 27  30  CD2   21  0.60  2.70  
 28  30  NE2   22  0.60  2.50  
 29  31  NE1   15  0.62  2.46  
 30  31  NE1   18  0.50  2.75  
 31  31  CE2   16  0.48  2.82  
 32  31  CD1   17  0.45  2.85  
 33  32  C     23  0.65  2.12  
 34  32  C     24  0.44  2.84  
 35  32  HD13  23  0.65  2.12  
 36  32  HD13  25  0.42  2.14  
 37  32  CD1   24  0.44  2.84  
 38  32  N     19  0.42  2.51  
 39  32  O     25  0.42  2.14  
 40  35  O     26  0.52  2.42  
 41  35  O     27  0.40  2.70  
 42  37  CG2   28  0.48  2.75  
 43  38  N     28  0.48  2.75  
 44  38  CD1   29  0.47  2.86  
 45  38  C     29  0.47  2.86  
 46  39  N     26  0.52  2.42  
 47  39  CB    27  0.40  2.70  
 48  40  CE1   30  0.57  2.87  
 49  40  CZ    31  0.44  3.00  
 50  40  O     32  0.42  2.68  
 51  44  CD2   30  0.57  2.87  
 52  44  CD2   31  0.44  3.00  
 53  44  CD2   32  0.42  2.68  
 54  46  O     33  0.52  2.42  
 55  47  O     11  0.42  2.37  
 56  48  N     33  0.52  2.42  
 57  49  N     10  0.50  2.41  
 58  53  HG11  34  0.69  1.64  
 59  53  HG13  35  0.40  2.29  
 60  54  HZ3   20  0.62  2.13  
 61  54  NZ    21  0.60  2.70  
 62  54  NZ    22  0.60  2.50  
 63  54  N     35  0.40  2.29  
 64  55  HD12  34  0.69  1.64  
 65  55  O      3  0.53  2.42  
 66  56  OD1    2  0.43  2.37  
 67  60  NH1    4  0.40  2.84  
 68  67  O     36  0.54  2.41  
 69  71  N     36  0.54  2.41  
 70  72  NH1   37  0.63  2.47  
 71  72  NH1   38  0.53  2.77  
 72  72  NH1   39  0.52  2.77  
 73  72  CZ    40  0.51  2.73  
 74  72  CZ    41  0.45  3.00  
 75  73  O     42  0.43  2.50  
 76  75  CD2    7  0.65  2.09  
 77  75  CD2    8  0.60  2.70  
 78  75  NE2    9  0.60  2.50  
 79  76  NE1   37  0.63  2.47  
 80  76  NE1   40  0.51  2.73  
 81  76  CE2   38  0.53  2.77  
 82  76  CE2   41  0.45  3.00  
 83  76  CD1   39  0.52  2.77  
 84  77  HD13  43  0.66  2.11  
 85  77  HD13  44  0.41  2.14  
 86  77  C     43  0.66  2.11  
 87  77  C     45  0.40  2.83  
 88  77  N     42  0.43  2.50  
 89  77  O     44  0.41  2.14  
 90  77  CD1   45  0.40  2.83  
 91  80  O     46  0.52  2.42  
 92  82  CG2   47  0.48  2.76  
 93  83  CD1   48  0.49  2.86  
 94  83  C     48  0.49  2.86  
 95  83  N     47  0.48  2.76  
 96  84  N     46  0.52  2.42  
 97  85  CE1   49  0.57  2.88  
 98  85  CZ    50  0.45  3.00  
 99  85  O     51  0.42  2.68  
100  89  CD2   49  0.57  2.88  
101  89  CD2   50  0.45  3.00  
102  89  CD2   51  0.42  2.68  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
