data_1DCD

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1DCD
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1DCD
_pdbx_vrpt_summary.PDB_deposition_date         1999-03-20
_pdbx_vrpt_summary.PDB_revision_number         6
_pdbx_vrpt_summary.PDB_revision_date           2023-08-09
_pdbx_vrpt_summary.report_creation_date        2023-08-02:09:51
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,mogul,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "PROTEIN (DESULFOREDOXIN)"  
2  non-polymer  "CADMIUM ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  3  
F  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  2.0  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
1  1  1   22.35  141614     ?     ?  
2  2  1   18.51    9178  2.00  2.00  
3  1  2  100.00  138981     ?     ?  
4  2  2  100.00    9054  2.00  2.00  
5  1  3   22.98  138945     ?     ?  
6  2  3   18.91    9053  2.00  2.00  
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  A  100.00  
2  4  2  A  1  1  A  100.00  
3  5  3  A  1  1  A   15.93  
4  6  3  A  1  1  A   11.38  
5  3  2  B  1  1  B  100.00  
6  4  2  B  1  1  B  100.00  
7  5  3  B  1  1  B   37.58  
8  6  3  B  1  1  B   36.87  
#
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  0.74  0.30  270  358  
2  1  1  B  B  0.77  0.30  270  359  
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       5.17
_pdbx_vrpt_summary_geometry.clashscore                     11.62
_pdbx_vrpt_summary_geometry.num_H_reduce                   511
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 540
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.30
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                717
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.76
#
_pdbx_vrpt_summary_diffraction.exp_method           x-ray
_pdbx_vrpt_summary_diffraction.ordinal              1
_pdbx_vrpt_summary_diffraction.PDB_resolution_high  2.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_low   14.80
_pdbx_vrpt_summary_diffraction.PDB_R                0.19
#
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  ALA  A    1  .  ?        ?  
  2  1  1  A   2  ASN  A    2  .  ?        1  
  3  1  1  A   3  GLU  A    3  .  ?        ?  
  4  1  1  A   4  GLY  A    4  .  ?        ?  
  5  1  1  A   5  ASP  A    5  .  ?        1  
  6  1  1  A   6  VAL  A    6  .  ?        ?  
  7  1  1  A   7  TYR  A    7  .  ?        ?  
  8  1  1  A   8  LYS  A    8  A  ?        ?  
  9  1  1  A   8  LYS  A    8  B  ?        ?  
 10  1  1  A   9  CYS  A    9  .  ?        ?  
 11  1  1  A  10  GLU  A   10  .  ?        ?  
 12  1  1  A  11  LEU  A   11  .  ?        ?  
 13  1  1  A  12  CYS  A   12  .  ?        ?  
 14  1  1  A  13  GLY  A   13  .  ?        ?  
 15  1  1  A  14  GLN  A   14  .  ?        ?  
 16  1  1  A  15  VAL  A   15  .  ?        2  
 17  1  1  A  16  VAL  A   16  .  ?        ?  
 18  1  1  A  17  LYS  A   17  .  ?        ?  
 19  1  1  A  18  VAL  A   18  .  ?        ?  
 20  1  1  A  19  LEU  A   19  .  ?        ?  
 21  1  1  A  20  GLU  A   20  .  ?        ?  
 22  1  1  A  21  GLU  A   21  .  ?        ?  
 23  1  1  A  22  GLY  A   22  .  ?        ?  
 24  1  1  A  23  GLY  A   23  .  ?        ?  
 25  1  1  A  24  GLY  A   24  .  ?        ?  
 26  1  1  A  25  THR  A   25  .  ?        ?  
 27  1  1  A  26  LEU  A   26  .  ?        ?  
 28  1  1  A  27  VAL  A   27  .  ?        ?  
 29  1  1  A  28  CYS  A   28  .  ?        ?  
 30  1  1  A  29  CYS  A   29  .  ?        ?  
 31  1  1  A  30  GLY  A   30  .  ?        ?  
 32  1  1  A  31  GLU  A   31  .  ?        ?  
 33  1  1  A  32  ASP  A   32  .  ?        ?  
 34  1  1  A  33  MET  A   33  .  ?        ?  
 35  1  1  A  34  VAL  A   34  .  ?        ?  
 36  1  1  A  35  LYS  A   35  .  ?        ?  
 37  1  1  A  36  GLN  A   36  .  ?        ?  
 38  1  1  B   1  ALA  B    1  .  ?        ?  
 39  1  1  B   2  ASN  B    2  .  ?        4  
 40  1  1  B   3  GLU  B    3  .  ?        ?  
 41  1  1  B   4  GLY  B    4  .  ?        2  
 42  1  1  B   5  ASP  B    5  .  ?        1  
 43  1  1  B   6  VAL  B    6  .  ?        ?  
 44  1  1  B   7  TYR  B    7  .  ?        ?  
 45  1  1  B   8  LYS  B    8  .  ?        ?  
 46  1  1  B   9  CYS  B    9  .  ?        ?  
 47  1  1  B  10  GLU  B   10  A  ?        1  
 48  1  1  B  10  GLU  B   10  B  ?        ?  
 49  1  1  B  11  LEU  B   11  .  ?        2  
 50  1  1  B  12  CYS  B   12  .  ?        ?  
 51  1  1  B  13  GLY  B   13  .  ?        ?  
 52  1  1  B  14  GLN  B   14  .  ?        ?  
 53  1  1  B  15  VAL  B   15  .  ?        ?  
 54  1  1  B  16  VAL  B   16  .  ?        ?  
 55  1  1  B  17  LYS  B   17  .  ?        2  
 56  1  1  B  18  VAL  B   18  .  ?        ?  
 57  1  1  B  19  LEU  B   19  .  ?        ?  
 58  1  1  B  20  GLU  B   20  .  ?        2  
 59  1  1  B  21  GLU  B   21  .  ?        ?  
 60  1  1  B  22  GLY  B   22  .  ?        ?  
 61  1  1  B  23  GLY  B   23  .  ?        ?  
 62  1  1  B  24  GLY  B   24  .  ?        ?  
 63  1  1  B  25  THR  B   25  .  ?        ?  
 64  1  1  B  26  LEU  B   26  .  ?        ?  
 65  1  1  B  27  VAL  B   27  .  ?        ?  
 66  1  1  B  28  CYS  B   28  .  ?        ?  
 67  1  1  B  29  CYS  B   29  .  ?        1  
 68  1  1  B  30  GLY  B   30  .  ?        ?  
 69  1  1  B  31  GLU  B   31  .  ?        1  
 70  1  1  B  32  ASP  B   32  .  ?        ?  
 71  1  1  B  33  MET  B   33  .  ?        ?  
 72  1  1  B  34  VAL  B   34  .  ?        1  
 73  1  1  B  35  LYS  B   35  .  ?        ?  
 74  1  1  B  36  GLN  B   36  .  ?        2  
 75  1  2  C   .  CD   A   37  .  ?        ?  
 76  1  2  D   .  CD   B   37  .  ?        ?  
 77  1  3  E   .  HOH  A  100  .  ?        ?  
 78  1  3  E   .  HOH  A  101  .  ?        ?  
 79  1  3  E   .  HOH  A  102  .  ?        ?  
 80  1  3  E   .  HOH  A  106  .  ?        ?  
 81  1  3  E   .  HOH  A  107  .  ?        ?  
 82  1  3  E   .  HOH  A  108  .  ?        ?  
 83  1  3  E   .  HOH  A  114  .  ?        ?  
 84  1  3  E   .  HOH  A  116  .  ?        ?  
 85  1  3  E   .  HOH  A  118  .  ?        ?  
 86  1  3  E   .  HOH  A  120  .  ?        ?  
 87  1  3  E   .  HOH  A  121  .  ?        ?  
 88  1  3  E   .  HOH  A  122  .  ?        ?  
 89  1  3  E   .  HOH  A  124  .  ?        ?  
 90  1  3  E   .  HOH  A  125  .  ?        ?  
 91  1  3  E   .  HOH  A  126  .  ?        ?  
 92  1  3  E   .  HOH  A  130  .  ?        ?  
 93  1  3  E   .  HOH  A  131  .  ?        ?  
 94  1  3  E   .  HOH  A  132  .  ?        ?  
 95  1  3  E   .  HOH  A  135  .  ?        ?  
 96  1  3  E   .  HOH  A  136  .  ?        ?  
 97  1  3  E   .  HOH  A  137  .  ?        ?  
 98  1  3  E   .  HOH  A  141  .  ?        ?  
 99  1  3  E   .  HOH  A  142  .  ?        ?  
100  1  3  E   .  HOH  A  143  .  ?        ?  
101  1  3  E   .  HOH  A  144  .  ?        ?  
102  1  3  E   .  HOH  A  145  .  ?        ?  
103  1  3  E   .  HOH  A  146  .  ?        ?  
104  1  3  E   .  HOH  A  147  .  ?        ?  
105  1  3  E   .  HOH  A  150  .  ?        ?  
106  1  3  E   .  HOH  A  152  .  ?        ?  
107  1  3  F   .  HOH  B  103  .  ?        ?  
108  1  3  F   .  HOH  B  104  .  ?        ?  
109  1  3  F   .  HOH  B  105  .  ?        ?  
110  1  3  F   .  HOH  B  109  .  ?        ?  
111  1  3  F   .  HOH  B  110  .  ?        ?  
112  1  3  F   .  HOH  B  111  .  ?        ?  
113  1  3  F   .  HOH  B  112  .  ?        ?  
114  1  3  F   .  HOH  B  113  .  ?        1  
115  1  3  F   .  HOH  B  115  .  ?        ?  
116  1  3  F   .  HOH  B  117  .  ?        ?  
117  1  3  F   .  HOH  B  119  .  ?        ?  
118  1  3  F   .  HOH  B  123  .  ?        ?  
119  1  3  F   .  HOH  B  127  .  ?        ?  
120  1  3  F   .  HOH  B  128  .  ?        ?  
121  1  3  F   .  HOH  B  129  .  ?        ?  
122  1  3  F   .  HOH  B  133  .  ?        ?  
123  1  3  F   .  HOH  B  134  .  ?        ?  
124  1  3  F   .  HOH  B  138  .  ?        ?  
125  1  3  F   .  HOH  B  139  .  ?        ?  
126  1  3  F   .  HOH  B  140  .  ?        ?  
127  1  3  F   .  HOH  B  148  .  ?        ?  
128  1  3  F   .  HOH  B  149  .  ?        ?  
129  1  3  F   .  HOH  B  151  .  ?        ?  
#
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.flippable_sidechain
_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  ?             ?      ?  ?           ?   7   5  0.25   7  0.26  molprobity  
 2   2  m120      -99.7  155.5  Favored     ?   6   8  0.31  11  0.87  molprobity  
 3   3  tt0       -53.7  131.4  Favored     ?   6   9  0.47  12  0.84  molprobity  
 4   4  ?          87.4   -3.1  Favored     ?   3   4  0.14   5  0.79  molprobity  
 5   5  m-20      -75.4  145.7  Favored     ?   4   8  0.27  11  0.80  molprobity  
 6   6  t        -115.6  131.0  Favored     ?   9   7  0.17  10  0.50  molprobity  
 7   7  m-85     -124.3  140.0  Favored     ?   9  13  0.28  18  0.71  molprobity  
 8   8  tttt     -129.0  143.7  Favored     ?   5   9  0.27  11  0.84  molprobity  
 9   9  tttt     -129.0  143.7  Favored     ?   5   9  0.27  11  0.84  molprobity  
10  10  t         -91.0  123.6  Favored     ?   4   6  0.26   8  0.91  molprobity  
11  11  mt-10     -82.7   -3.3  Favored     ?   6   9  0.36  12  0.76  molprobity  
12  12  mt        -94.0  -44.4  Favored     ?  11   8  0.22  11  0.41  molprobity  
13  13  p        -115.5   -5.3  Favored     ?   4   6  0.24   8  0.75  molprobity  
14  14  ?          79.4    5.6  Favored     ?   3   4  0.25   5  0.59  molprobity  
15  15  tt0       -63.5  132.8  Favored     ?   8   9  0.27  12  0.64  molprobity  
16  16  t        -125.4  127.5  Favored     ?   9   7  0.18  10  0.64  molprobity  
17  17  m        -127.6  156.6  Favored     ?   9   7  0.21  10  0.69  molprobity  
18  18  OUTLIER  -118.3  136.2  Favored     ?  13   9  0.28  11  0.58  molprobity  
19  19  t         -78.1  117.2  Favored     ?   9   7  0.13  10  0.37  molprobity  
20  20  mt        -86.4  -41.6  Favored     ?  11   8  0.21  11  0.35  molprobity  
21  21  mm-40    -131.4  128.3  Favored     ?   6   9  0.28  12  0.61  molprobity  
22  22  OUTLIER   -80.5  142.3  Favored     ?   6   9  0.35  12  1.29  molprobity  
23  23  ?        -137.8  174.3  Favored     ?   3   4  0.64   5  0.77  molprobity  
24  24  ?         -92.3   -9.5  Favored     ?   3   4  0.32   5  1.22  molprobity  
25  25  ?         -74.8  159.7  Favored     ?   3   4  0.37   5  0.73  molprobity  
26  26  m         -93.3  125.8  Favored     ?   7   7  0.34  10  0.78  molprobity  
27  27  mt        -72.2  132.8  Favored     ?  11   8  0.22  11  0.40  molprobity  
28  28  t        -126.5  143.8  Favored     ?   9   7  0.28  10  0.93  molprobity  
29  29  t        -148.0  139.5  Favored     ?   4   6  0.21   8  0.58  molprobity  
30  30  m          52.5   33.7  Favored     ?   4   6  0.23   8  0.84  molprobity  
31  31  ?          63.9   14.5  Favored     ?   3   4  0.25   5  0.48  molprobity  
32  32  mm-40    -119.7  151.6  Favored     ?   6   9  0.28  12  0.93  molprobity  
33  33  m-20      -62.2  130.2  Favored     ?   4   8  0.24  11  0.67  molprobity  
34  34  mtp       -69.4  155.0  Favored     ?   9   8  0.42  10  0.71  molprobity  
35  35  t         -97.4  126.8  Favored     ?   9   7  0.16  10  0.84  molprobity  
36  36  tttt      -65.1  116.3  Favored     ?  13   9  0.32  11  0.84  molprobity  
37  37  mm100         ?      ?  ?           ?   8   9  0.49   9  0.52  molprobity  
38  38  ?             ?      ?  ?           ?   7   5  0.19   7  0.94  molprobity  
39  39  m120     -122.6  165.5  Favored     1   6   8  0.34  11  0.60  molprobity  
40  40  tt0       -62.6  134.5  Favored     ?   6   9  0.09  12  0.48  molprobity  
41  41  ?          87.1  -11.8  Favored     ?   3   4  0.22   5  0.67  molprobity  
42  42  m-20      -69.5  142.7  Favored     ?   4   8  0.26  11  0.55  molprobity  
43  43  t        -115.9  123.7  Favored     ?   9   7  0.13  10  0.54  molprobity  
44  44  m-85     -117.5  147.6  Favored     ?   9  13  0.31  18  0.95  molprobity  
45  45  tttt     -133.0  145.6  Favored     ?  13   9  0.33  11  0.59  molprobity  
46  46  t         -94.7  123.6  Favored     ?   4   6  0.17   8  0.89  molprobity  
47  47  mt-10     -81.0  -14.4  Favored     ?   2   9  0.17  12  0.68  molprobity  
48  48  mt-10     -81.0  -14.4  Favored     ?   2   9  0.17  12  0.68  molprobity  
49  49  mt        -83.1  -45.4  Favored     ?  11   8  0.29  11  0.71  molprobity  
50  50  p        -119.7   -6.0  Favored     ?   4   6  0.20   8  1.16  molprobity  
51  51  ?          75.1   16.2  Favored     ?   3   4  0.31   5  0.46  molprobity  
52  52  tt0       -71.1  139.0  Favored     ?   8   9  0.36  12  0.76  molprobity  
53  53  t        -127.4  132.2  Favored     ?   9   7  0.21  10  0.77  molprobity  
54  54  m        -130.9  152.6  Favored     ?   9   7  0.22  10  0.79  molprobity  
55  55  tttp     -106.0  132.2  Favored     ?  13   9  0.32  11  0.86  molprobity  
56  56  t         -74.9  118.3  Favored     ?   9   7  0.28  10  0.99  molprobity  
57  57  mt        -92.8  -43.2  Favored     ?  11   8  0.21  11  0.44  molprobity  
58  58  mm-40    -129.2  120.7  Favored     ?   6   9  0.34  12  0.99  molprobity  
59  59  OUTLIER   -76.5  149.2  Favored     ?   6   9  0.23  12  1.00  molprobity  
60  60  ?        -159.9  166.6  Favored     ?   3   4  0.44   5  1.05  molprobity  
61  61  ?         -87.0   -0.6  Favored     ?   3   4  0.60   5  1.25  molprobity  
62  62  ?         -76.0  156.1  Favored     ?   3   4  0.36   5  0.49  molprobity  
63  63  m         -91.2  124.7  Favored     ?   7   7  0.30  10  0.96  molprobity  
64  64  mt        -75.3  132.0  Favored     ?  11   8  0.23  11  0.60  molprobity  
65  65  t        -130.0  143.1  Favored     ?   9   7  0.24  10  0.82  molprobity  
66  66  t        -147.7  140.5  Favored     ?   4   6  0.29   8  0.74  molprobity  
67  67  m          50.2   36.8  Favored     ?   4   6  0.19   8  0.63  molprobity  
68  68  ?          60.6   17.6  Favored     ?   3   4  0.38   5  0.49  molprobity  
69  69  mm-40    -125.3  154.2  Favored     ?   6   9  0.29  12  0.95  molprobity  
70  70  m-20      -60.7  127.5  Favored     ?   4   8  0.20  11  0.59  molprobity  
71  71  mtp       -67.8  154.2  Favored     ?   9   8  0.39  10  0.87  molprobity  
72  72  t        -107.0  125.4  Favored     ?   9   7  0.23  10  0.64  molprobity  
73  73  ttpt      -63.1  134.9  Favored     ?  13   9  0.27  11  0.48  molprobity  
74  74  mm-40         ?      ?  ?           ?   8   9  0.61   9  0.55  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    2  O      1  0.43  2.18  
 2    5  HB2    1  0.43  2.18  
 3   16  HB     2  0.80  1.63  
 4   16  CB     3  0.50  2.38  
 5   39  O      4  0.50  2.11  
 6   39  ND2    5  0.44  2.51  
 7   39  HD22   6  0.41  1.61  
 8   39  HA     6  0.41  1.61  
 9   41  HA2    7  0.88  1.56  
10   41  HA2    8  0.53  2.32  
11   42  HB2    4  0.50  2.11  
12   47  CD     9  0.41  2.41  
13   49  HD12  10  0.56  1.87  
14   49  HD11  11  0.47  1.97  
15   55  HE3    7  0.88  1.56  
16   55  CE     8  0.53  2.32  
17   58  HB2    2  0.80  1.63  
18   58  HB2    3  0.50  2.38  
19   67  HB2   10  0.56  1.87  
20   69  HG2   11  0.47  1.97  
21   72  HG21   9  0.41  2.41  
22   74  NE2   12  0.42  2.33  
23   74  HA    12  0.42  2.33  
24  114  O      5  0.44  2.51  
#
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  mogul        unknown                                                               Y  
3  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
