data_1DHG

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1DHG
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1DHG
_pdbx_vrpt_summary.PDB_deposition_date         1999-03-22
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2023-08-09
_pdbx_vrpt_summary.report_creation_date        2023-08-02:11:30
_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  "MERCURY (II) 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  2.5  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   42.80  141614     ?     ?  
2  2  1   62.53    5346  2.50  2.50  
3  1  2  100.00  138981     ?     ?  
4  2  2  100.00    5231  2.50  2.50  
5  1  3   60.43  138945     ?     ?  
6  2  3   82.38    5233  2.50  2.50  
#
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  100.00  
4  6  3  A  1  1  A  100.00  
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   36.59  
8  6  3  B  1  1  B   63.06  
#
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  0.63  0.46  261  347  
2  1  1  B  B  0.65  0.46  261  347  
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       1.72
_pdbx_vrpt_summary_geometry.clashscore                     6.81
_pdbx_vrpt_summary_geometry.num_H_reduce                   504
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 522
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.46
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                694
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.64
#
_pdbx_vrpt_summary_diffraction.exp_method           x-ray
_pdbx_vrpt_summary_diffraction.ordinal              1
_pdbx_vrpt_summary_diffraction.PDB_resolution_high  2.50
_pdbx_vrpt_summary_diffraction.PDB_resolution_low   23.50
_pdbx_vrpt_summary_diffraction.PDB_R                0.18
#
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  
 2  1  1  A   2  ASN  A   2  .  ?        ?  
 3  1  1  A   3  GLU  A   3  .  ?        ?  
 4  1  1  A   4  GLY  A   4  .  ?        ?  
 5  1  1  A   5  ASP  A   5  .  ?        ?  
 6  1  1  A   6  VAL  A   6  .  ?        ?  
 7  1  1  A   7  TYR  A   7  .  ?        ?  
 8  1  1  A   8  LYS  A   8  .  ?        ?  
 9  1  1  A   9  CYS  A   9  .  ?        ?  
10  1  1  A  10  GLU  A  10  .  ?        ?  
11  1  1  A  11  LEU  A  11  .  ?        ?  
12  1  1  A  12  CYS  A  12  .  ?        ?  
13  1  1  A  13  GLY  A  13  .  ?        ?  
14  1  1  A  14  GLN  A  14  .  ?        1  
15  1  1  A  15  VAL  A  15  .  ?        ?  
16  1  1  A  16  VAL  A  16  .  ?        ?  
17  1  1  A  17  LYS  A  17  .  ?        ?  
18  1  1  A  18  VAL  A  18  .  ?        ?  
19  1  1  A  19  LEU  A  19  .  ?        1  
20  1  1  A  20  GLU  A  20  .  ?        ?  
21  1  1  A  21  GLU  A  21  .  ?        1  
22  1  1  A  22  GLY  A  22  .  ?        1  
23  1  1  A  23  GLY  A  23  .  ?        ?  
24  1  1  A  24  GLY  A  24  .  ?        ?  
25  1  1  A  25  THR  A  25  .  ?        ?  
26  1  1  A  26  LEU  A  26  .  ?        ?  
27  1  1  A  27  VAL  A  27  .  ?        ?  
28  1  1  A  28  CYS  A  28  .  ?        ?  
29  1  1  A  29  CYS  A  29  .  ?        ?  
30  1  1  A  30  GLY  A  30  .  ?        ?  
31  1  1  A  31  GLU  A  31  .  ?        ?  
32  1  1  A  32  ASP  A  32  .  ?        ?  
33  1  1  A  33  MET  A  33  .  ?        ?  
34  1  1  A  34  VAL  A  34  .  ?        ?  
35  1  1  A  35  LYS  A  35  .  ?        ?  
36  1  1  A  36  GLN  A  36  .  ?        ?  
37  1  1  B   1  ALA  B   1  .  ?        1  
38  1  1  B   2  ASN  B   2  .  ?        ?  
39  1  1  B   3  GLU  B   3  .  ?        ?  
40  1  1  B   4  GLY  B   4  .  ?        1  
41  1  1  B   5  ASP  B   5  .  ?        ?  
42  1  1  B   6  VAL  B   6  .  ?        ?  
43  1  1  B   7  TYR  B   7  .  ?        ?  
44  1  1  B   8  LYS  B   8  .  ?        ?  
45  1  1  B   9  CYS  B   9  .  ?        ?  
46  1  1  B  10  GLU  B  10  .  ?        ?  
47  1  1  B  11  LEU  B  11  .  ?        ?  
48  1  1  B  12  CYS  B  12  .  ?        ?  
49  1  1  B  13  GLY  B  13  .  ?        ?  
50  1  1  B  14  GLN  B  14  .  ?        2  
51  1  1  B  15  VAL  B  15  .  ?        ?  
52  1  1  B  16  VAL  B  16  .  ?        ?  
53  1  1  B  17  LYS  B  17  .  ?        2  
54  1  1  B  18  VAL  B  18  .  ?        ?  
55  1  1  B  19  LEU  B  19  .  ?        ?  
56  1  1  B  20  GLU  B  20  .  ?        ?  
57  1  1  B  21  GLU  B  21  .  ?        1  
58  1  1  B  22  GLY  B  22  .  ?        1  
59  1  1  B  23  GLY  B  23  .  ?        ?  
60  1  1  B  24  GLY  B  24  .  ?        ?  
61  1  1  B  25  THR  B  25  .  ?        ?  
62  1  1  B  26  LEU  B  26  .  ?        ?  
63  1  1  B  27  VAL  B  27  .  ?        ?  
64  1  1  B  28  CYS  B  28  .  ?        ?  
65  1  1  B  29  CYS  B  29  .  ?        ?  
66  1  1  B  30  GLY  B  30  .  ?        ?  
67  1  1  B  31  GLU  B  31  .  ?        ?  
68  1  1  B  32  ASP  B  32  .  ?        ?  
69  1  1  B  33  MET  B  33  .  ?        ?  
70  1  1  B  34  VAL  B  34  .  ?        ?  
71  1  1  B  35  LYS  B  35  .  ?        ?  
72  1  1  B  36  GLN  B  36  .  ?        ?  
73  1  2  C   .  HG   A  37  .  ?        ?  
74  1  2  D   .  HG   B  37  .  ?        ?  
75  1  3  E   .  HOH  A  38  .  ?        ?  
76  1  3  E   .  HOH  A  39  .  ?        ?  
77  1  3  E   .  HOH  A  40  .  ?        ?  
78  1  3  E   .  HOH  A  41  .  ?        ?  
79  1  3  E   .  HOH  A  42  .  ?        ?  
80  1  3  E   .  HOH  A  43  .  ?        ?  
81  1  3  F   .  HOH  B  38  .  ?        ?  
82  1  3  F   .  HOH  B  39  .  ?        ?  
83  1  3  F   .  HOH  B  40  .  ?        ?  
84  1  3  F   .  HOH  B  41  .  ?        ?  
85  1  3  F   .  HOH  B  42  .  ?        ?  
86  1  3  F   .  HOH  B  43  .  ?        ?  
87  1  3  F   .  HOH  B  44  .  ?        ?  
#
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  0.88   7  0.13  molprobity  
 2   2  m-80      -87.1  157.3  Favored     ?   6   8  0.44  11  0.70  molprobity  
 3   3  tt0       -64.5  133.2  Favored     ?   6   9  0.23  12  0.42  molprobity  
 4   4  ?          95.1  -23.6  Favored     ?   3   4  0.39   5  0.22  molprobity  
 5   5  m-20      -61.3  149.5  Favored     ?   4   8  0.28  11  0.77  molprobity  
 6   6  t        -114.5  131.7  Favored     ?   9   7  0.40  10  0.74  molprobity  
 7   7  m-85     -121.4  141.2  Favored     ?   9  13  0.57  18  0.49  molprobity  
 8   8  tttt     -123.7  143.8  Favored     ?  13   9  0.40  11  0.80  molprobity  
 9   9  t        -101.6  112.0  Favored     ?   4   6  0.48   8  0.96  molprobity  
10  10  mt-10     -65.8  -15.2  Favored     ?   6   9  0.25  12  0.69  molprobity  
11  11  mt        -84.2  -28.1  Favored     ?  11   8  0.20  11  0.56  molprobity  
12  12  p        -134.2    0.3  Favored     ?   4   6  0.18   8  0.54  molprobity  
13  13  ?          69.7   15.0  Favored     ?   3   4  0.32   5  1.08  molprobity  
14  14  tt0       -71.1  131.9  Favored     ?   8   9  0.42  12  0.49  molprobity  
15  15  t        -118.2  136.4  Favored     ?   9   7  0.30  10  0.54  molprobity  
16  16  m        -134.4  154.3  Favored     ?   9   7  0.78  10  0.50  molprobity  
17  17  tttt     -118.3  132.4  Favored     ?  13   9  0.29  11  0.78  molprobity  
18  18  t         -77.0  116.3  Favored     ?   9   7  0.34  10  0.56  molprobity  
19  19  mt        -88.8  -41.8  Favored     ?  11   8  0.36  11  0.34  molprobity  
20  20  mm-40    -124.6  124.7  Favored     ?   6   9  0.64  12  0.70  molprobity  
21  21  tt0       -64.3  140.6  Favored     ?   6   9  0.97  12  0.41  molprobity  
22  22  ?        -146.9  165.5  Favored     ?   3   4  0.29   5  0.66  molprobity  
23  23  ?         -88.4  -14.5  Favored     ?   3   4  0.21   5  0.98  molprobity  
24  24  ?         -77.4  157.5  Favored     ?   3   4  0.22   5  0.41  molprobity  
25  25  m         -90.8  129.9  Favored     ?   7   7  0.39  10  0.73  molprobity  
26  26  mt        -72.8  123.7  Favored     ?  11   8  0.25  11  0.75  molprobity  
27  27  t        -121.8  147.8  Favored     ?   9   7  0.40  10  0.61  molprobity  
28  28  t        -155.9  138.7  Favored     ?   4   6  0.13   8  0.65  molprobity  
29  29  m          54.4   35.7  Favored     ?   4   6  0.38   8  0.53  molprobity  
30  30  ?          70.7   -0.9  Favored     ?   3   4  0.36   5  0.64  molprobity  
31  31  mm-40    -119.3  151.1  Favored     ?   6   9  0.86  12  0.43  molprobity  
32  32  m-20      -61.9  132.5  Favored     ?   4   8  0.22  11  0.77  molprobity  
33  33  mtp       -73.5  148.8  Favored     ?   9   8  0.30  10  0.66  molprobity  
34  34  t         -93.6  133.0  Favored     ?   9   7  0.23  10  0.80  molprobity  
35  35  tttt      -72.3  130.3  Favored     ?  13   9  0.31  11  0.45  molprobity  
36  36  mm100         ?      ?  ?           ?   8   9  0.61   9  0.43  molprobity  
37  37  ?             ?      ?  ?           ?   7   5  0.97   7  0.20  molprobity  
38  38  m120      -84.0  156.8  Favored     ?   6   8  0.34  11  0.83  molprobity  
39  39  tt0       -65.5  133.8  Favored     ?   6   9  0.28  12  0.29  molprobity  
40  40  ?          95.2  -23.7  Favored     ?   3   4  0.33   5  0.24  molprobity  
41  41  m-20      -59.1  150.9  Favored     ?   4   8  0.25  11  0.56  molprobity  
42  42  t        -118.6  131.5  Favored     ?   9   7  0.56  10  0.53  molprobity  
43  43  m-85     -120.5  139.9  Favored     ?   9  13  0.62  18  0.44  molprobity  
44  44  tttt     -126.3  144.1  Favored     ?  13   9  0.35  11  0.38  molprobity  
45  45  t        -102.6  115.1  Favored     ?   4   6  0.33   8  0.75  molprobity  
46  46  mt-10     -64.5  -18.5  Favored     ?   6   9  0.57  12  0.69  molprobity  
47  47  mt        -83.3  -26.0  Favored     ?  11   8  0.41  11  1.37  molprobity  
48  48  OUTLIER  -133.2   -2.9  Favored     ?   4   6  0.47   8  0.65  molprobity  
49  49  ?          69.0   17.7  Favored     ?   3   4  0.29   5  0.97  molprobity  
50  50  tt0       -75.5  134.8  Favored     1   8   9  0.21  12  0.48  molprobity  
51  51  t        -119.3  138.4  Favored     ?   9   7  0.60  10  0.53  molprobity  
52  52  m        -135.9  155.4  Favored     ?   9   7  0.38  10  0.52  molprobity  
53  53  tttt     -117.7  133.8  Favored     ?  13   9  0.31  11  0.44  molprobity  
54  54  t         -76.2  113.7  Favored     ?   9   7  0.53  10  0.51  molprobity  
55  55  mt        -87.7  -43.4  Favored     ?  11   8  0.33  11  0.73  molprobity  
56  56  mm-40    -125.8  126.2  Favored     ?   6   9  0.38  12  0.65  molprobity  
57  57  tt0       -64.5  140.4  Favored     ?   6   9  0.91  12  0.76  molprobity  
58  58  ?        -147.3  166.2  Favored     ?   3   4  0.39   5  0.63  molprobity  
59  59  ?         -88.6  -14.9  Favored     ?   3   4  0.22   5  0.96  molprobity  
60  60  ?         -76.0  156.5  Favored     ?   3   4  0.27   5  0.42  molprobity  
61  61  m         -90.9  128.7  Favored     ?   7   7  0.29  10  0.44  molprobity  
62  62  mt        -73.4  124.2  Favored     ?  11   8  0.27  11  0.67  molprobity  
63  63  t        -122.4  145.9  Favored     ?   9   7  0.73  10  0.57  molprobity  
64  64  t        -155.1  139.8  Favored     ?   4   6  0.18   8  0.61  molprobity  
65  65  m          55.1   34.3  Favored     ?   4   6  0.18   8  0.60  molprobity  
66  66  ?          72.5   -1.8  Favored     ?   3   4  0.37   5  0.66  molprobity  
67  67  mm-40    -119.7  153.5  Favored     ?   6   9  0.50  12  0.69  molprobity  
68  68  m-20      -61.8  131.9  Favored     ?   4   8  0.27  11  0.78  molprobity  
69  69  mtp       -73.2  148.9  Favored     ?   9   8  0.42  10  0.72  molprobity  
70  70  t         -94.6  131.8  Favored     ?   9   7  0.19  10  0.77  molprobity  
71  71  tttt      -70.2  128.8  Favored     ?  13   9  0.32  11  0.49  molprobity  
72  72  mm-40         ?      ?  ?           ?   8   9  0.66   9  0.54  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  HB3   1  0.65  1.61  
 2   1  O     2  0.44  2.17  
 3  14  HB2   3  0.46  1.98  
 4  19  HD11  4  0.65  1.78  
 5  21  HG3   2  0.44  2.17  
 6  22  HA3   5  0.57  1.86  
 7  37  O     6  0.49  2.12  
 8  40  HA2   7  0.58  1.85  
 9  50  HE22  1  0.65  1.61  
10  50  HB2   5  0.57  1.86  
11  53  HB2   4  0.65  1.78  
12  53  HE2   7  0.58  1.85  
13  57  HG3   6  0.49  2.12  
14  58  HA3   3  0.46  1.98  
#
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  
##
