0.018144
0.000000
0.008573
0.000000
0.026989
0.000000
0.000000
0.000000
0.017054
0.00000
0.00000
0.00000
Bhowmick, T.
Ramagopal, U.A.
Ghosh, S.
Nagaraja, V.
Ramakumar, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
115.29
90.00
55.115
37.052
64.854
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Mn 2
54.938
MANGANESE (II) ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
MN
N
237
N
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
Y
247
N
C
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
N
265
N
C
N
266
N
C
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
N
C
N
282
N
O
N
283
N
O
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
R
C
N
296
N
O
N
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
C
N
314
N
C
N
315
N
O
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
UK
Nat Commun
2041-1723
5
4124
4124
10.1038/ncomms5124
24916461
Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors
2014
10.2210/pdb4dky/pdb
pdb_00004dky
100
1
Mirrors
CCD
2010-10-29
ADSC QUANTUM 315
Double Crystal Monochromator (Cryogenically cooled)
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
X29A
NSLS
0.979
SYNCHROTRON
NSLS BEAMLINE X29A
11598.211
DNA-binding protein HU homolog
N-terminal Bacterial histone-like domain, UNP residues 1-100
2
man
polymer
54.938
MANGANESE (II) ION
2
syn
non-polymer
18.015
water
42
nat
water
no
no
MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFR
PGAQFKAVVSGAQRLPAEGPHHHHHH
MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFR
PGAQFKAVVSGAQRLPAEGPHHHHHH
A,B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
1
106
hupB
419947
Mycobacterium tuberculosis H37Ra
562
Escherichia coli
BL21(DE3)plysS
Plasmid
Biological sequence
pET20b
1
2.58
52.35
VAPOR DIFFUSION, HANGING DROP
6.7
0.1M Tris-HCl, pH 6.7, 2.5M sodium formate, 10mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
295
database_2
entity_name_com
entity_src_gen
pdbx_database_related
struct
struct_conn
struct_ref
struct_ref_seq
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Database references
Database references
Derived calculations
Source and taxonomy
Structure summary
Data collection
Refinement description
1
0
2013-02-06
1
1
2014-08-27
1
2
2023-07-26
1
3
2023-11-08
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity_src_gen.gene_src_strain
_entity_src_gen.pdbx_beg_seq_num
_entity_src_gen.pdbx_end_seq_num
_entity_src_gen.pdbx_gene_src_gene
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
_entity_src_gen.pdbx_gene_src_scientific_name
_entity_src_gen.pdbx_seq_type
_pdbx_database_related.details
_struct.title
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_ref.db_code
_struct_ref.pdbx_db_accession
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
PDBJ
2012-02-05
REL
REL
MN
MANGANESE (II) ION
HOH
water
3C4I
PDB ENTRY 3C4I
PDB
experimental model
MN
98
2
MN
MN
201
A
MN
105
2
MN
MN
201
B
HOH
1
3
HOH
HOH
301
A
HOH
3
3
HOH
HOH
302
A
HOH
4
3
HOH
HOH
303
A
HOH
6
3
HOH
HOH
304
A
HOH
8
3
HOH
HOH
305
A
HOH
9
3
HOH
HOH
306
A
HOH
10
3
HOH
HOH
307
A
HOH
11
3
HOH
HOH
308
A
HOH
12
3
HOH
HOH
309
A
HOH
17
3
HOH
HOH
310
A
HOH
18
3
HOH
HOH
311
A
HOH
19
3
HOH
HOH
312
A
HOH
20
3
HOH
HOH
313
A
HOH
21
3
HOH
HOH
314
A
HOH
22
3
HOH
HOH
315
A
HOH
23
3
HOH
HOH
316
A
HOH
25
3
HOH
HOH
317
A
HOH
27
3
HOH
HOH
318
A
HOH
28
3
HOH
HOH
319
A
HOH
29
3
HOH
HOH
320
A
HOH
30
3
HOH
HOH
321
A
HOH
32
3
HOH
HOH
322
A
HOH
33
3
HOH
HOH
323
A
HOH
34
3
HOH
HOH
324
A
HOH
37
3
HOH
HOH
325
A
HOH
38
3
HOH
HOH
326
A
HOH
39
3
HOH
HOH
327
A
HOH
40
3
HOH
HOH
328
A
HOH
41
3
HOH
HOH
329
A
HOH
2
3
HOH
HOH
301
B
HOH
5
3
HOH
HOH
302
B
HOH
7
3
HOH
HOH
303
B
HOH
13
3
HOH
HOH
304
B
HOH
14
3
HOH
HOH
305
B
HOH
15
3
HOH
HOH
306
B
HOH
16
3
HOH
HOH
307
B
HOH
24
3
HOH
HOH
308
B
HOH
26
3
HOH
HOH
309
B
HOH
31
3
HOH
HOH
310
B
HOH
35
3
HOH
HOH
311
B
HOH
36
3
HOH
HOH
312
B
HOH
42
3
HOH
HOH
313
B
4.000
4.000
31.920
31.920
Phaser MODE: MR_AUTO
MET
1
n
1
MET
1
A
ASN
2
n
2
ASN
2
A
LYS
3
n
3
LYS
3
A
ALA
4
n
4
ALA
4
A
GLU
5
n
5
GLU
5
A
LEU
6
n
6
LEU
6
A
ILE
7
n
7
ILE
7
A
ASP
8
n
8
ASP
8
A
VAL
9
n
9
VAL
9
A
LEU
10
n
10
LEU
10
A
THR
11
n
11
THR
11
A
GLN
12
n
12
GLN
12
A
LYS
13
n
13
LYS
13
A
LEU
14
n
14
LEU
14
A
GLY
15
n
15
GLY
15
A
SER
16
n
16
SER
16
A
ASP
17
n
17
ASP
17
A
ARG
18
n
18
ARG
18
A
ARG
19
n
19
ARG
19
A
GLN
20
n
20
GLN
20
A
ALA
21
n
21
ALA
21
A
THR
22
n
22
THR
22
A
ALA
23
n
23
ALA
23
A
ALA
24
n
24
ALA
24
A
VAL
25
n
25
VAL
25
A
GLU
26
n
26
GLU
26
A
ASN
27
n
27
ASN
27
A
VAL
28
n
28
VAL
28
A
VAL
29
n
29
VAL
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
ILE
32
n
32
ILE
32
A
VAL
33
n
33
VAL
33
A
ARG
34
n
34
ARG
34
A
ALA
35
n
35
ALA
35
A
VAL
36
n
36
VAL
36
A
HIS
37
n
37
HIS
37
A
LYS
38
n
38
LYS
38
A
GLY
39
n
39
GLY
39
A
ASP
40
n
40
ASP
40
A
SER
41
n
41
SER
41
A
VAL
42
n
42
VAL
42
A
THR
43
n
43
THR
43
A
ILE
44
n
44
ILE
44
A
THR
45
n
45
THR
45
A
GLY
46
n
46
GLY
46
A
PHE
47
n
47
PHE
47
A
GLY
48
n
48
GLY
48
A
VAL
49
n
49
VAL
49
A
PHE
50
n
50
PHE
50
A
GLU
51
n
51
GLU
51
A
GLN
52
n
52
GLN
52
A
ARG
53
n
53
ARG
53
A
ARG
54
n
54
ARG
54
A
ARG
55
n
55
ARG
55
A
ALA
56
n
56
ALA
56
A
ALA
57
n
57
ALA
57
A
ARG
58
n
58
ARG
58
A
VAL
59
n
59
VAL
59
A
ALA
60
n
60
ALA
60
A
ARG
61
n
61
ARG
61
A
ASN
62
n
62
ASN
62
A
PRO
63
n
63
PRO
63
A
ARG
64
n
64
ARG
64
A
THR
65
n
65
THR
65
A
GLY
66
n
66
GLY
66
A
GLU
67
n
67
GLU
67
A
THR
68
n
68
THR
68
A
VAL
69
n
69
VAL
69
A
LYS
70
n
70
LYS
70
A
VAL
71
n
71
VAL
71
A
LYS
72
n
72
LYS
72
A
PRO
73
n
73
PRO
73
A
THR
74
n
74
THR
74
A
SER
75
n
75
SER
75
A
VAL
76
n
76
VAL
76
A
PRO
77
n
77
PRO
77
A
ALA
78
n
78
ALA
78
A
PHE
79
n
79
PHE
79
A
ARG
80
n
80
ARG
80
A
PRO
81
n
81
PRO
81
A
GLY
82
n
82
GLY
82
A
ALA
83
n
83
ALA
83
A
GLN
84
n
84
GLN
84
A
PHE
85
n
85
PHE
85
A
LYS
86
n
86
LYS
86
A
ALA
87
n
87
ALA
87
A
VAL
88
n
88
VAL
88
A
VAL
89
n
89
VAL
89
A
SER
90
n
90
SER
90
A
GLY
91
n
91
GLY
91
A
ALA
92
n
92
ALA
92
A
GLN
93
n
93
GLN
93
A
ARG
94
n
94
ARG
94
A
LEU
95
n
95
LEU
95
A
PRO
96
n
96
PRO
96
A
ALA
97
n
97
ALA
97
A
n
98
98
A
n
99
99
A
n
100
100
A
n
101
101
A
n
102
102
A
n
103
103
A
n
104
104
A
n
105
105
A
n
106
106
A
MET
1
n
1
MET
1
B
ASN
2
n
2
ASN
2
B
LYS
3
n
3
LYS
3
B
ALA
4
n
4
ALA
4
B
GLU
5
n
5
GLU
5
B
LEU
6
n
6
LEU
6
B
ILE
7
n
7
ILE
7
B
ASP
8
n
8
ASP
8
B
VAL
9
n
9
VAL
9
B
LEU
10
n
10
LEU
10
B
THR
11
n
11
THR
11
B
GLN
12
n
12
GLN
12
B
LYS
13
n
13
LYS
13
B
LEU
14
n
14
LEU
14
B
GLY
15
n
15
GLY
15
B
SER
16
n
16
SER
16
B
ASP
17
n
17
ASP
17
B
ARG
18
n
18
ARG
18
B
ARG
19
n
19
ARG
19
B
GLN
20
n
20
GLN
20
B
ALA
21
n
21
ALA
21
B
THR
22
n
22
THR
22
B
ALA
23
n
23
ALA
23
B
ALA
24
n
24
ALA
24
B
VAL
25
n
25
VAL
25
B
GLU
26
n
26
GLU
26
B
ASN
27
n
27
ASN
27
B
VAL
28
n
28
VAL
28
B
VAL
29
n
29
VAL
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
ILE
32
n
32
ILE
32
B
VAL
33
n
33
VAL
33
B
ARG
34
n
34
ARG
34
B
ALA
35
n
35
ALA
35
B
VAL
36
n
36
VAL
36
B
HIS
37
n
37
HIS
37
B
LYS
38
n
38
LYS
38
B
GLY
39
n
39
GLY
39
B
ASP
40
n
40
ASP
40
B
SER
41
n
41
SER
41
B
VAL
42
n
42
VAL
42
B
THR
43
n
43
THR
43
B
ILE
44
n
44
ILE
44
B
THR
45
n
45
THR
45
B
GLY
46
n
46
GLY
46
B
PHE
47
n
47
PHE
47
B
GLY
48
n
48
GLY
48
B
VAL
49
n
49
VAL
49
B
PHE
50
n
50
PHE
50
B
GLU
51
n
51
GLU
51
B
GLN
52
n
52
GLN
52
B
ARG
53
n
53
ARG
53
B
ARG
54
n
54
ARG
54
B
ARG
55
n
55
ARG
55
B
ALA
56
n
56
ALA
56
B
ALA
57
n
57
ALA
57
B
ARG
58
n
58
ARG
58
B
VAL
59
n
59
VAL
59
B
ALA
60
n
60
ALA
60
B
ARG
61
n
61
ARG
61
B
ASN
62
n
62
ASN
62
B
PRO
63
n
63
PRO
63
B
ARG
64
n
64
ARG
64
B
THR
65
n
65
THR
65
B
GLY
66
n
66
GLY
66
B
GLU
67
n
67
GLU
67
B
THR
68
n
68
THR
68
B
VAL
69
n
69
VAL
69
B
LYS
70
n
70
LYS
70
B
VAL
71
n
71
VAL
71
B
LYS
72
n
72
LYS
72
B
PRO
73
n
73
PRO
73
B
THR
74
n
74
THR
74
B
SER
75
n
75
SER
75
B
VAL
76
n
76
VAL
76
B
PRO
77
n
77
PRO
77
B
ALA
78
n
78
ALA
78
B
PHE
79
n
79
PHE
79
B
ARG
80
n
80
ARG
80
B
PRO
81
n
81
PRO
81
B
GLY
82
n
82
GLY
82
B
ALA
83
n
83
ALA
83
B
GLN
84
n
84
GLN
84
B
PHE
85
n
85
PHE
85
B
LYS
86
n
86
LYS
86
B
ALA
87
n
87
ALA
87
B
VAL
88
n
88
VAL
88
B
VAL
89
n
89
VAL
89
B
SER
90
n
90
SER
90
B
GLY
91
n
91
GLY
91
B
ALA
92
n
92
ALA
92
B
GLN
93
n
93
GLN
93
B
ARG
94
n
94
ARG
94
B
LEU
95
n
95
LEU
95
B
PRO
96
n
96
PRO
96
B
ALA
97
n
97
ALA
97
B
GLU
98
n
98
GLU
98
B
n
99
99
B
n
100
100
B
n
101
101
B
HIS
102
n
102
HIS
102
B
HIS
103
n
103
HIS
103
B
HIS
104
n
104
HIS
104
B
n
105
105
B
n
106
106
B
2.2215
-1.9222
1.8877
2.2639
-2.6349
3.2745
-0.1616
0.1478
0.2105
-0.0152
0.0327
-0.1576
0.1143
-0.1359
0.1289
0.2149
-0.0426
0.1638
0.1649
0.0096
0.2361
refined
-7.7387
-31.0439
-5.3211
X-RAY DIFFRACTION
1.5792
1.1631
2.4023
4.4186
4.7041
6.0777
0.0415
-0.1945
-0.2864
0.5563
0.2129
-0.0143
0.4653
-0.0119
-0.2544
0.2605
-0.0339
0.1273
0.1732
0.0079
0.1912
refined
-1.0637
-25.7445
8.1226
X-RAY DIFFRACTION
5.5138
-0.4037
1.6404
2.9677
-0.5169
0.5501
0.1279
-0.0958
-0.0984
0.2136
-0.1094
-0.4129
-0.0102
-0.0509
-0.0185
0.1924
0.0054
0.1528
0.2166
0.0679
0.2747
refined
6.1285
-13.7737
4.3846
X-RAY DIFFRACTION
22.1432
-7.1903
5.4691
6.6963
-0.0379
2.0502
-0.6065
-0.2910
1.1725
0.4167
0.1093
-0.0370
-0.0491
-0.0957
0.4972
0.1683
0.0033
0.1288
0.1754
-0.0279
0.2612
refined
-9.2122
4.6653
13.7469
X-RAY DIFFRACTION
0.6101
0.6336
-1.7549
1.2591
0.6581
15.4484
-0.0416
-0.0342
0.0111
-0.1653
0.0514
0.0227
-0.4196
0.2716
-0.0097
0.2099
0.0321
0.1384
0.1911
0.0113
0.1247
refined
4.2447
-11.7673
-3.0169
X-RAY DIFFRACTION
14.6097
-17.7185
-25.7763
21.5462
31.3137
45.5259
0.0904
1.1552
-1.1206
-0.2283
-1.7494
1.2792
-0.4272
-2.1323
1.6590
0.9867
-0.2501
-0.0656
0.3150
0.0458
0.3354
refined
5.9849
-18.4504
-18.6728
X-RAY DIFFRACTION
2.0499
0.9966
-0.7703
6.8212
-2.2872
0.8678
-0.0103
-0.1995
0.0240
-0.1194
-0.0513
-0.2703
0.0274
0.0497
0.0616
0.1855
0.0310
0.1142
0.1568
0.0271
0.1570
refined
-20.2310
-6.1183
-5.6180
X-RAY DIFFRACTION
2.9326
3.3924
-1.2187
8.4206
-3.2088
2.5444
0.3112
-0.3113
0.0656
0.7389
-0.2781
-0.1851
-0.3860
0.0902
-0.0331
0.2441
0.0029
0.1258
0.1507
-0.0317
0.1442
refined
-25.7971
-10.2552
7.3279
X-RAY DIFFRACTION
2.0701
-2.2977
1.6446
11.1903
-5.3304
3.1735
0.1613
0.0609
-0.1806
-0.2084
0.0031
0.3476
0.1590
0.0766
-0.1644
0.1656
0.0583
0.1040
0.1719
-0.0139
0.1410
refined
-33.6408
-22.9006
4.2965
X-RAY DIFFRACTION
1.8082
-0.7433
-1.2493
11.1063
0.7293
0.8693
-1.0009
-0.3548
0.1645
0.1237
1.0888
-0.3649
0.7027
0.2489
-0.0879
0.6278
0.1411
0.0338
0.3282
-0.1381
0.2945
refined
-18.0105
-41.7328
13.4924
X-RAY DIFFRACTION
0.0417
-0.1094
-0.0838
1.1775
1.0767
0.9931
-0.0161
-0.0643
-0.0459
-0.2240
-0.0646
0.0973
-0.2293
-0.1049
0.0807
0.2360
0.0344
0.1445
0.2251
-0.0028
0.1702
refined
-31.5757
-25.6393
-2.2711
X-RAY DIFFRACTION
28.2178
4.6010
-0.5199
3.5348
5.6787
11.9398
-1.0160
-0.1133
-0.3925
-0.8019
-0.2574
0.5777
-1.3342
-0.3825
1.2734
0.4832
0.0818
0.0080
0.0168
-0.0243
0.2216
refined
-30.9366
-19.4688
-20.6017
X-RAY DIFFRACTION
A
1
A
18
X-RAY DIFFRACTION
1
A
19
A
40
X-RAY DIFFRACTION
2
A
41
A
54
X-RAY DIFFRACTION
3
A
55
A
73
X-RAY DIFFRACTION
4
A
74
A
90
X-RAY DIFFRACTION
5
A
91
A
97
X-RAY DIFFRACTION
6
B
1
B
17
X-RAY DIFFRACTION
7
B
18
B
40
X-RAY DIFFRACTION
8
B
41
B
54
X-RAY DIFFRACTION
9
B
55
B
72
X-RAY DIFFRACTION
10
B
73
B
91
X-RAY DIFFRACTION
11
B
92
B
104
X-RAY DIFFRACTION
12
1
0.593
2
0.407
author_and_software_defined_assembly
PISA
2
dimeric
author_and_software_defined_assembly
PISA
2
dimeric
4470
-51
11670
4490
-51
12310
B
GLU
98
B
OE1
GLU
98
1_555
B
MN
201
D
MN
MN
1_555
B
GLU
98
B
OE2
GLU
98
1_555
60.0
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_455
-x-1,y,-z
crystal symmetry operation
-55.1150000000
0.0000000000
0.0000000000
A
N
VAL
42
A
N
VAL
42
A
O
PHE
50
A
O
PHE
50
A
N
ARG
53
A
N
ARG
53
A
O
VAL
76
A
O
VAL
76
A
N
ALA
60
A
N
ALA
60
A
O
VAL
69
A
O
VAL
69
B
N
ILE
44
B
N
ILE
44
B
O
GLY
48
B
O
GLY
48
B
N
ARG
53
B
N
ARG
53
B
O
VAL
76
B
O
VAL
76
B
N
ALA
60
B
N
ALA
60
B
O
VAL
69
B
O
VAL
69
1
B
CG
HIS
102
B
CG
HIS
102
1
Y
1
B
ND1
HIS
102
B
ND1
HIS
102
1
Y
1
B
CD2
HIS
102
B
CD2
HIS
102
1
Y
1
B
CE1
HIS
102
B
CE1
HIS
102
1
Y
1
B
NE2
HIS
102
B
NE2
HIS
102
1
Y
1
A
GLU
98
A
GLU
98
1
Y
1
A
GLY
99
A
GLY
99
1
Y
1
A
PRO
100
A
PRO
100
1
Y
1
A
HIS
101
A
HIS
101
1
Y
1
A
HIS
102
A
HIS
102
1
Y
1
A
HIS
103
A
HIS
103
1
Y
1
A
HIS
104
A
HIS
104
1
Y
1
A
HIS
105
A
HIS
105
1
Y
1
A
HIS
106
A
HIS
106
1
Y
1
B
GLY
99
B
GLY
99
1
Y
1
B
PRO
100
B
PRO
100
1
Y
1
B
HIS
101
B
HIS
101
1
Y
1
B
HIS
105
B
HIS
105
1
Y
1
B
HIS
106
B
HIS
106
1
Y
1
A
PHE
47
-127.27
-77.74
1
B
PHE
47
-106.43
-66.99
1
B
HIS
103
-117.97
70.96
55.087
-24.93
0.00
-3.36
-9.90
-0.00
34.83
0.945
0.906
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.24786
0.18314
0.18596
2.478
31.92
336
6667
4.8
80.90
1.000
1.000
15.309
0.177
0.1989
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.191
0.068
0.80
0.80
1.20
PDB ENTRY 3C4I
MAXIMUM LIKELIHOOD
MASK
2.478
31.92
42
1550
2
0
1506
0.026
0.019
1525
0.003
0.020
1082
2.390
1.948
2058
3.844
3.000
2609
7.227
5.000
195
38.065
21.642
67
22.732
15.000
264
18.191
15.000
22
0.133
0.200
242
0.008
0.021
1697
0.007
0.020
321
0.313
0.228
2.542
18
214
20
38.16
2.478
50.000
4DKY
8601
8546
2.0
2.0
0.094
1
7.600
3.800
81.3
0.575
2.478
2.542
1
3.600
99.000
0.636
2.542
2.590
1
3.700
99.800
0.492
2.590
2.640
1
3.600
100.000
0.466
2.640
2.690
1
3.800
99.800
0.406
2.690
2.750
1
3.800
100.000
0.373
2.750
2.820
1
3.800
100.000
0.236
2.820
2.890
1
3.900
100.000
0.283
2.890
2.960
1
3.800
100.000
0.186
2.960
3.050
1
3.800
100.000
0.186
3.050
3.150
1
3.900
100.000
0.136
3.150
3.260
1
3.800
100.000
0.140
3.260
3.390
1
3.900
100.000
0.102
3.390
3.550
1
3.800
100.000
0.081
3.550
3.730
1
3.800
100.000
0.074
3.730
3.970
1
3.700
100.000
0.058
3.970
4.270
1
3.700
100.000
0.049
4.270
4.700
1
3.700
100.000
0.047
4.700
5.380
1
3.500
100.000
0.047
5.380
6.780
1
3.800
100.000
0.043
6.780
50.000
1
3.500
98.900
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
program
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
program
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Wed Jun 29 17:49:14 2011 (svn )
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.3.0
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
data collection
CBASS
Crystal structure Analysis of N terminal region containing the dimerization domain and DNA binding domain of HU protein(Histone like protein-DNA binding) from Mycobacterium tuberculosis [H37Ra]
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
A
ASN
2
A
ASN
2
HELX_P
A
GLY
15
A
GLY
15
1
1
14
A
ASP
17
A
ASP
17
HELX_P
A
LYS
38
A
LYS
38
1
2
22
A
GLY
82
A
GLY
82
HELX_P
A
SER
90
A
SER
90
1
3
9
B
ASN
2
B
ASN
2
HELX_P
B
GLY
15
B
GLY
15
1
4
14
B
ASP
17
B
ASP
17
HELX_P
B
LYS
38
B
LYS
38
1
5
22
B
GLY
82
B
GLY
82
HELX_P
B
SER
90
B
SER
90
1
6
9
metalc
2.355
A
MN
201
C
MN
MN
1_555
A
HOH
322
E
O
HOH
1_555
metalc
2.140
B
GLU
98
B
OE1
GLU
98
1_555
B
MN
201
D
MN
MN
1_555
metalc
2.319
B
GLU
98
B
OE2
GLU
98
1_555
B
MN
201
D
MN
MN
1_555
DNA BINDING PROTEIN
Nucleoid Associated protein, Nucleoid architecture, Histone-like, HU, HU-IHF fold, genome compaction, gene regulation, DNA BINDING PROTEIN
A5U6Z7_MYCTA
UNP
1
1
A5U6Z7
MNKAELIDVLTQKLGSDRRQATAAVENVVDTIVRAVHKGDSVTITGFGVFEQRRRAARVARNPRTGETVKVKPTSVPAFR
PGAQFKAVVSGAQRLPAEGP
1
100
4DKY
1
100
A5U6Z7
A
1
1
100
1
100
4DKY
1
100
A5U6Z7
B
1
1
100
1
expression tag
HIS
101
4DKY
A
A5U6Z7
UNP
101
1
expression tag
HIS
102
4DKY
A
A5U6Z7
UNP
102
1
expression tag
HIS
103
4DKY
A
A5U6Z7
UNP
103
1
expression tag
HIS
104
4DKY
A
A5U6Z7
UNP
104
1
expression tag
HIS
105
4DKY
A
A5U6Z7
UNP
105
1
expression tag
HIS
106
4DKY
A
A5U6Z7
UNP
106
2
expression tag
HIS
101
4DKY
B
A5U6Z7
UNP
101
2
expression tag
HIS
102
4DKY
B
A5U6Z7
UNP
102
2
expression tag
HIS
103
4DKY
B
A5U6Z7
UNP
103
2
expression tag
HIS
104
4DKY
B
A5U6Z7
UNP
104
2
expression tag
HIS
105
4DKY
B
A5U6Z7
UNP
105
2
expression tag
HIS
106
4DKY
B
A5U6Z7
UNP
106
3
2
3
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
42
A
VAL
42
A
ILE
44
A
ILE
44
A
GLY
48
A
GLY
48
A
ARG
55
A
ARG
55
A
THR
74
A
THR
74
A
PRO
81
A
PRO
81
A
ARG
58
A
ARG
58
A
ARG
61
A
ARG
61
A
THR
68
A
THR
68
A
VAL
71
A
VAL
71
B
VAL
42
B
VAL
42
B
ILE
44
B
ILE
44
B
GLY
48
B
GLY
48
B
ARG
55
B
ARG
55
B
THR
74
B
THR
74
B
PRO
81
B
PRO
81
B
ARG
58
B
ARG
58
B
ARG
61
B
ARG
61
B
THR
68
B
THR
68
B
VAL
71
B
VAL
71
BINDING SITE FOR RESIDUE MN A 201
A
MN
201
Software
2
BINDING SITE FOR RESIDUE MN B 201
B
MN
201
Software
3
A
ARG
94
A
ARG
94
2
1_555
A
HOH
322
E
HOH
2
1_555
B
ARG
94
B
ARG
94
3
1_555
B
GLU
98
B
GLU
98
3
1_555
B
HIS
104
B
HIS
104
3
1_555
3
P 1 2 1