0.00738
0.00000
0.00000
0.00000
0.00738
0.00000
0.00000
0.00000
0.02812
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
135.560
135.560
35.560
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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C4 H10 O2
90.121
2-ETHOXYETHANOL
non-polymer
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
Na 1
22.990
SODIUM 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
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
UNKNOWN LIGAND
non-polymer
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
To be published
0353
Crystal structure of DNA polymerase III, gamma subunit-related protein (tm0771) from Thermotoga maritima at 2.00 A resolution
10.2210/pdb2gno/pdb
pdb_00002gno
100
1
Flat mirror (vertical focusing)
CCD
2005-12-18
ADSC QUANTUM 315
Single crystal Si(111) bent monochromator (horizontal focusing)
MAD
M
x-ray
1
0.979224
1.0
0.918370
1.0
0.978940
1.0
BL11-1
SSRL
0.979224, 0.918370, 0.978940
SYNCHROTRON
SSRL BEAMLINE BL11-1
35485.527
DNA polymerase III, gamma subunit-related protein
residues 9-312
1
man
polymer
22.990
SODIUM ION
1
syn
non-polymer
UNKNOWN LIGAND
1
syn
non-polymer
90.121
2-ETHOXYETHANOL
2
syn
non-polymer
18.015
water
107
nat
water
no
yes
GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPEL
YTRKYVIVHDCER(MSE)TQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLW
EELPLLERDFKTALEAYKLGAEKLSGL(MSE)ESLKVLETEKLLKKVLSKGLEGYLACRELLERFSKVESKEFFALFDQV
TNTITGKDAFLLIQRLTRIILHENTWESVEDQKSVSFLDSILRVKIANLNNKLTL(MSE)NILAIHRERKRGVNAWS
GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPEL
YTRKYVIVHDCERMTQQAANAFLKALEEPPEYAVIVLNTRRWHYLLPTIKSRVFRVVVNVPKEFRDLVKEKIGDLWEELP
LLERDFKTALEAYKLGAEKLSGLMESLKVLETEKLLKKVLSKGLEGYLACRELLERFSKVESKEFFALFDQVTNTITGKD
AFLLIQRLTRIILHENTWESVEDQKSVSFLDSILRVKIANLNNKLTLMNILAIHRERKRGVNAWS
A
360384
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
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
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
Thermotoga
Thermotoga maritima
MSB8
Escherichia
sample
tm0771
243274
Thermotoga maritima
562
Escherichia coli
Plasmid
1
2.31
46.22
VAPOR DIFFUSION, SITTING DROP, NANODROP
6.2
35.0% 2-ethoxyethanol, 0.2M NaCl, 0.1M Na,K-Phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Advisory
Source and taxonomy
Version format compliance
Database references
Derived calculations
1
0
2006-04-18
1
1
2008-05-01
1
2
2011-07-13
1
3
2023-01-25
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
SEQUENCE:
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION
TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV
PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY
RESIDUES 9-312 OF THE TM0771 SEQUENCE. A SMALL
AMOUNT OF PROTEIN WITH THE TAG UNCLEAVED REMAINED
IN THE SAMPLE AFTER PURIFICATION. A SERIES OF
DIFFERENT LENGTH N-TERMINAL TRUNCATIONS WERE TRIED
TO IMPROVE DIFFRACTION QUALITY FROM THIS TARGET.
THE CONSTRUCT WITH RESIDUES 1-8 ELIMINATED PRODUCED
THE BEST DIFFRACTING CRYSTAL.
Y
RCSB
Y
RCSB
2006-04-10
REL
REL
NA
SODIUM ION
UNL
UNKNOWN LIGAND
ETX
2-ETHOXYETHANOL
HOH
water
NA
2
2
NA
NA
2
A
UNL
1
3
UNL
UNL
1
A
ETX
3
4
ETX
ETX
3
A
ETX
4
4
ETX
ETX
4
A
HOH
5
5
HOH
HOH
313
A
HOH
6
5
HOH
HOH
314
A
HOH
7
5
HOH
HOH
315
A
HOH
8
5
HOH
HOH
316
A
HOH
9
5
HOH
HOH
317
A
HOH
10
5
HOH
HOH
318
A
HOH
11
5
HOH
HOH
319
A
HOH
12
5
HOH
HOH
320
A
HOH
13
5
HOH
HOH
321
A
HOH
14
5
HOH
HOH
322
A
HOH
15
5
HOH
HOH
323
A
HOH
16
5
HOH
HOH
324
A
HOH
17
5
HOH
HOH
325
A
HOH
18
5
HOH
HOH
326
A
HOH
19
5
HOH
HOH
327
A
HOH
20
5
HOH
HOH
328
A
HOH
21
5
HOH
HOH
329
A
HOH
22
5
HOH
HOH
330
A
HOH
23
5
HOH
HOH
331
A
HOH
24
5
HOH
HOH
332
A
HOH
25
5
HOH
HOH
333
A
HOH
26
5
HOH
HOH
334
A
HOH
27
5
HOH
HOH
335
A
HOH
28
5
HOH
HOH
336
A
HOH
29
5
HOH
HOH
337
A
HOH
30
5
HOH
HOH
338
A
HOH
31
5
HOH
HOH
339
A
HOH
33
5
HOH
HOH
340
A
HOH
34
5
HOH
HOH
341
A
HOH
35
5
HOH
HOH
342
A
HOH
36
5
HOH
HOH
343
A
HOH
37
5
HOH
HOH
344
A
HOH
38
5
HOH
HOH
345
A
HOH
39
5
HOH
HOH
346
A
HOH
40
5
HOH
HOH
347
A
HOH
42
5
HOH
HOH
348
A
HOH
44
5
HOH
HOH
349
A
HOH
45
5
HOH
HOH
350
A
HOH
46
5
HOH
HOH
351
A
HOH
47
5
HOH
HOH
352
A
HOH
48
5
HOH
HOH
353
A
HOH
49
5
HOH
HOH
354
A
HOH
50
5
HOH
HOH
355
A
HOH
51
5
HOH
HOH
356
A
HOH
52
5
HOH
HOH
357
A
HOH
53
5
HOH
HOH
358
A
HOH
54
5
HOH
HOH
359
A
HOH
55
5
HOH
HOH
360
A
HOH
56
5
HOH
HOH
361
A
HOH
57
5
HOH
HOH
362
A
HOH
58
5
HOH
HOH
363
A
HOH
59
5
HOH
HOH
364
A
HOH
60
5
HOH
HOH
365
A
HOH
61
5
HOH
HOH
366
A
HOH
62
5
HOH
HOH
367
A
HOH
63
5
HOH
HOH
368
A
HOH
64
5
HOH
HOH
369
A
HOH
65
5
HOH
HOH
370
A
HOH
66
5
HOH
HOH
371
A
HOH
67
5
HOH
HOH
372
A
HOH
68
5
HOH
HOH
373
A
HOH
69
5
HOH
HOH
374
A
HOH
70
5
HOH
HOH
375
A
HOH
71
5
HOH
HOH
376
A
HOH
72
5
HOH
HOH
377
A
HOH
73
5
HOH
HOH
378
A
HOH
74
5
HOH
HOH
379
A
HOH
75
5
HOH
HOH
380
A
HOH
76
5
HOH
HOH
381
A
HOH
78
5
HOH
HOH
382
A
HOH
79
5
HOH
HOH
383
A
HOH
80
5
HOH
HOH
384
A
HOH
81
5
HOH
HOH
385
A
HOH
82
5
HOH
HOH
386
A
HOH
83
5
HOH
HOH
387
A
HOH
84
5
HOH
HOH
388
A
HOH
85
5
HOH
HOH
389
A
HOH
86
5
HOH
HOH
390
A
HOH
87
5
HOH
HOH
391
A
HOH
88
5
HOH
HOH
392
A
HOH
89
5
HOH
HOH
393
A
HOH
90
5
HOH
HOH
394
A
HOH
91
5
HOH
HOH
395
A
HOH
92
5
HOH
HOH
396
A
HOH
93
5
HOH
HOH
397
A
HOH
94
5
HOH
HOH
398
A
HOH
95
5
HOH
HOH
399
A
HOH
96
5
HOH
HOH
400
A
HOH
97
5
HOH
HOH
401
A
HOH
98
5
HOH
HOH
402
A
HOH
99
5
HOH
HOH
403
A
HOH
100
5
HOH
HOH
404
A
HOH
101
5
HOH
HOH
405
A
HOH
102
5
HOH
HOH
406
A
HOH
103
5
HOH
HOH
407
A
HOH
104
5
HOH
HOH
408
A
HOH
105
5
HOH
HOH
409
A
HOH
106
5
HOH
HOH
410
A
HOH
107
5
HOH
HOH
411
A
HOH
108
5
HOH
HOH
412
A
HOH
109
5
HOH
HOH
413
A
HOH
110
5
HOH
HOH
414
A
HOH
112
5
HOH
HOH
415
A
HOH
113
5
HOH
HOH
416
A
HOH
114
5
HOH
HOH
417
A
HOH
116
5
HOH
HOH
418
A
HOH
117
5
HOH
HOH
419
A
n
1
8
A
n
2
9
A
n
3
10
A
ASP
11
n
4
ASP
11
A
GLN
12
n
5
GLN
12
A
LEU
13
n
6
LEU
13
A
GLU
14
n
7
GLU
14
A
THR
15
n
8
THR
15
A
LEU
16
n
9
LEU
16
A
LYS
17
n
10
LYS
17
A
ARG
18
n
11
ARG
18
A
ILE
19
n
12
ILE
19
A
ILE
20
n
13
ILE
20
A
GLU
21
n
14
GLU
21
A
LYS
22
n
15
LYS
22
A
SER
23
n
16
SER
23
A
GLU
24
n
17
GLU
24
A
GLY
25
n
18
GLY
25
A
ILE
26
n
19
ILE
26
A
SER
27
n
20
SER
27
A
ILE
28
n
21
ILE
28
A
LEU
29
n
22
LEU
29
A
ILE
30
n
23
ILE
30
A
ASN
31
n
24
ASN
31
A
GLY
32
n
25
GLY
32
A
GLU
33
n
26
GLU
33
A
ASP
34
n
27
ASP
34
A
LEU
35
n
28
LEU
35
A
SER
36
n
29
SER
36
A
TYR
37
n
30
TYR
37
A
PRO
38
n
31
PRO
38
A
ARG
39
n
32
ARG
39
A
GLU
40
n
33
GLU
40
A
VAL
41
n
34
VAL
41
A
SER
42
n
35
SER
42
A
LEU
43
n
36
LEU
43
A
GLU
44
n
37
GLU
44
A
LEU
45
n
38
LEU
45
A
PRO
46
n
39
PRO
46
A
GLU
47
n
40
GLU
47
A
TYR
48
n
41
TYR
48
A
VAL
49
n
42
VAL
49
A
GLU
50
n
43
GLU
50
A
LYS
51
n
44
LYS
51
A
PHE
52
n
45
PHE
52
A
PRO
53
n
46
PRO
53
A
PRO
54
n
47
PRO
54
A
LYS
55
n
48
LYS
55
A
ALA
56
n
49
ALA
56
A
SER
57
n
50
SER
57
A
ASP
58
n
51
ASP
58
A
VAL
59
n
52
VAL
59
A
LEU
60
n
53
LEU
60
A
GLU
61
n
54
GLU
61
A
ILE
62
n
55
ILE
62
A
ASP
63
n
56
ASP
63
A
PRO
64
n
57
PRO
64
A
GLU
65
n
58
GLU
65
A
GLY
66
n
59
GLY
66
A
GLU
67
n
60
GLU
67
A
ASN
68
n
61
ASN
68
A
ILE
69
n
62
ILE
69
A
GLY
70
n
63
GLY
70
A
ILE
71
n
64
ILE
71
A
ASP
72
n
65
ASP
72
A
ASP
73
n
66
ASP
73
A
ILE
74
n
67
ILE
74
A
ARG
75
n
68
ARG
75
A
THR
76
n
69
THR
76
A
ILE
77
n
70
ILE
77
A
LYS
78
n
71
LYS
78
A
ASP
79
n
72
ASP
79
A
PHE
80
n
73
PHE
80
A
LEU
81
n
74
LEU
81
A
ASN
82
n
75
ASN
82
A
TYR
83
n
76
TYR
83
A
SER
84
n
77
SER
84
A
PRO
85
n
78
PRO
85
A
GLU
86
n
79
GLU
86
A
LEU
87
n
80
LEU
87
A
TYR
88
n
81
TYR
88
A
THR
89
n
82
THR
89
A
ARG
90
n
83
ARG
90
A
LYS
91
n
84
LYS
91
A
TYR
92
n
85
TYR
92
A
VAL
93
n
86
VAL
93
A
ILE
94
n
87
ILE
94
A
VAL
95
n
88
VAL
95
A
HIS
96
n
89
HIS
96
A
ASP
97
n
90
ASP
97
A
CYS
98
n
91
CYS
98
A
GLU
99
n
92
GLU
99
A
ARG
100
n
93
ARG
100
A
MSE
101
n
94
MSE
101
A
THR
102
n
95
THR
102
A
GLN
103
n
96
GLN
103
A
GLN
104
n
97
GLN
104
A
ALA
105
n
98
ALA
105
A
ALA
106
n
99
ALA
106
A
ASN
107
n
100
ASN
107
A
ALA
108
n
101
ALA
108
A
PHE
109
n
102
PHE
109
A
LEU
110
n
103
LEU
110
A
LYS
111
n
104
LYS
111
A
ALA
112
n
105
ALA
112
A
LEU
113
n
106
LEU
113
A
GLU
114
n
107
GLU
114
A
GLU
115
n
108
GLU
115
A
PRO
116
n
109
PRO
116
A
PRO
117
n
110
PRO
117
A
GLU
118
n
111
GLU
118
A
TYR
119
n
112
TYR
119
A
ALA
120
n
113
ALA
120
A
VAL
121
n
114
VAL
121
A
ILE
122
n
115
ILE
122
A
VAL
123
n
116
VAL
123
A
LEU
124
n
117
LEU
124
A
ASN
125
n
118
ASN
125
A
THR
126
n
119
THR
126
A
ARG
127
n
120
ARG
127
A
ARG
128
n
121
ARG
128
A
TRP
129
n
122
TRP
129
A
HIS
130
n
123
HIS
130
A
TYR
131
n
124
TYR
131
A
LEU
132
n
125
LEU
132
A
LEU
133
n
126
LEU
133
A
PRO
134
n
127
PRO
134
A
THR
135
n
128
THR
135
A
ILE
136
n
129
ILE
136
A
LYS
137
n
130
LYS
137
A
SER
138
n
131
SER
138
A
ARG
139
n
132
ARG
139
A
VAL
140
n
133
VAL
140
A
PHE
141
n
134
PHE
141
A
ARG
142
n
135
ARG
142
A
VAL
143
n
136
VAL
143
A
VAL
144
n
137
VAL
144
A
VAL
145
n
138
VAL
145
A
ASN
146
n
139
ASN
146
A
VAL
147
n
140
VAL
147
A
PRO
148
n
141
PRO
148
A
LYS
149
n
142
LYS
149
A
GLU
150
n
143
GLU
150
A
PHE
151
n
144
PHE
151
A
ARG
152
n
145
ARG
152
A
ASP
153
n
146
ASP
153
A
LEU
154
n
147
LEU
154
A
VAL
155
n
148
VAL
155
A
LYS
156
n
149
LYS
156
A
GLU
157
n
150
GLU
157
A
LYS
158
n
151
LYS
158
A
ILE
159
n
152
ILE
159
A
GLY
160
n
153
GLY
160
A
ASP
161
n
154
ASP
161
A
LEU
162
n
155
LEU
162
A
TRP
163
n
156
TRP
163
A
GLU
164
n
157
GLU
164
A
GLU
165
n
158
GLU
165
A
LEU
166
n
159
LEU
166
A
PRO
167
n
160
PRO
167
A
LEU
168
n
161
LEU
168
A
LEU
169
n
162
LEU
169
A
GLU
170
n
163
GLU
170
A
ARG
171
n
164
ARG
171
A
ASP
172
n
165
ASP
172
A
PHE
173
n
166
PHE
173
A
LYS
174
n
167
LYS
174
A
THR
175
n
168
THR
175
A
ALA
176
n
169
ALA
176
A
LEU
177
n
170
LEU
177
A
GLU
178
n
171
GLU
178
A
ALA
179
n
172
ALA
179
A
TYR
180
n
173
TYR
180
A
LYS
181
n
174
LYS
181
A
LEU
182
n
175
LEU
182
A
GLY
183
n
176
GLY
183
A
ALA
184
n
177
ALA
184
A
GLU
185
n
178
GLU
185
A
LYS
186
n
179
LYS
186
A
LEU
187
n
180
LEU
187
A
SER
188
n
181
SER
188
A
GLY
189
n
182
GLY
189
A
LEU
190
n
183
LEU
190
A
MSE
191
n
184
MSE
191
A
GLU
192
n
185
GLU
192
A
SER
193
n
186
SER
193
A
LEU
194
n
187
LEU
194
A
LYS
195
n
188
LYS
195
A
VAL
196
n
189
VAL
196
A
LEU
197
n
190
LEU
197
A
GLU
198
n
191
GLU
198
A
THR
199
n
192
THR
199
A
GLU
200
n
193
GLU
200
A
LYS
201
n
194
LYS
201
A
LEU
202
n
195
LEU
202
A
LEU
203
n
196
LEU
203
A
LYS
204
n
197
LYS
204
A
LYS
205
n
198
LYS
205
A
VAL
206
n
199
VAL
206
A
LEU
207
n
200
LEU
207
A
SER
208
n
201
SER
208
A
LYS
209
n
202
LYS
209
A
GLY
210
n
203
GLY
210
A
LEU
211
n
204
LEU
211
A
GLU
212
n
205
GLU
212
A
GLY
213
n
206
GLY
213
A
TYR
214
n
207
TYR
214
A
LEU
215
n
208
LEU
215
A
ALA
216
n
209
ALA
216
A
CYS
217
n
210
CYS
217
A
ARG
218
n
211
ARG
218
A
GLU
219
n
212
GLU
219
A
LEU
220
n
213
LEU
220
A
LEU
221
n
214
LEU
221
A
GLU
222
n
215
GLU
222
A
ARG
223
n
216
ARG
223
A
PHE
224
n
217
PHE
224
A
SER
225
n
218
SER
225
A
LYS
226
n
219
LYS
226
A
VAL
227
n
220
VAL
227
A
GLU
228
n
221
GLU
228
A
SER
229
n
222
SER
229
A
LYS
230
n
223
LYS
230
A
GLU
231
n
224
GLU
231
A
PHE
232
n
225
PHE
232
A
PHE
233
n
226
PHE
233
A
ALA
234
n
227
ALA
234
A
LEU
235
n
228
LEU
235
A
PHE
236
n
229
PHE
236
A
ASP
237
n
230
ASP
237
A
GLN
238
n
231
GLN
238
A
VAL
239
n
232
VAL
239
A
THR
240
n
233
THR
240
A
ASN
241
n
234
ASN
241
A
THR
242
n
235
THR
242
A
ILE
243
n
236
ILE
243
A
THR
244
n
237
THR
244
A
GLY
245
n
238
GLY
245
A
LYS
246
n
239
LYS
246
A
ASP
247
n
240
ASP
247
A
ALA
248
n
241
ALA
248
A
PHE
249
n
242
PHE
249
A
LEU
250
n
243
LEU
250
A
LEU
251
n
244
LEU
251
A
ILE
252
n
245
ILE
252
A
GLN
253
n
246
GLN
253
A
ARG
254
n
247
ARG
254
A
LEU
255
n
248
LEU
255
A
THR
256
n
249
THR
256
A
ARG
257
n
250
ARG
257
A
ILE
258
n
251
ILE
258
A
ILE
259
n
252
ILE
259
A
LEU
260
n
253
LEU
260
A
HIS
261
n
254
HIS
261
A
GLU
262
n
255
GLU
262
A
ASN
263
n
256
ASN
263
A
THR
264
n
257
THR
264
A
TRP
265
n
258
TRP
265
A
GLU
266
n
259
GLU
266
A
SER
267
n
260
SER
267
A
VAL
268
n
261
VAL
268
A
GLU
269
n
262
GLU
269
A
ASP
270
n
263
ASP
270
A
GLN
271
n
264
GLN
271
A
LYS
272
n
265
LYS
272
A
SER
273
n
266
SER
273
A
VAL
274
n
267
VAL
274
A
SER
275
n
268
SER
275
A
PHE
276
n
269
PHE
276
A
LEU
277
n
270
LEU
277
A
ASP
278
n
271
ASP
278
A
SER
279
n
272
SER
279
A
ILE
280
n
273
ILE
280
A
LEU
281
n
274
LEU
281
A
ARG
282
n
275
ARG
282
A
VAL
283
n
276
VAL
283
A
LYS
284
n
277
LYS
284
A
ILE
285
n
278
ILE
285
A
ALA
286
n
279
ALA
286
A
ASN
287
n
280
ASN
287
A
LEU
288
n
281
LEU
288
A
ASN
289
n
282
ASN
289
A
ASN
290
n
283
ASN
290
A
LYS
291
n
284
LYS
291
A
LEU
292
n
285
LEU
292
A
THR
293
n
286
THR
293
A
LEU
294
n
287
LEU
294
A
MSE
295
n
288
MSE
295
A
ASN
296
n
289
ASN
296
A
ILE
297
n
290
ILE
297
A
LEU
298
n
291
LEU
298
A
ALA
299
n
292
ALA
299
A
ILE
300
n
293
ILE
300
A
HIS
301
n
294
HIS
301
A
ARG
302
n
295
ARG
302
A
GLU
303
n
296
GLU
303
A
ARG
304
n
297
ARG
304
A
LYS
305
n
298
LYS
305
A
ARG
306
n
299
ARG
306
A
n
300
307
A
n
301
308
A
n
302
309
A
n
303
310
A
n
304
311
A
n
305
312
A
2.2739
3.3447
-0.0458
6.0604
-2.5080
6.0805
-0.4766
0.8218
0.1320
-0.8650
0.6166
-0.1455
0.0443
-1.0041
-0.1401
-0.0210
-0.0383
-0.0224
0.1935
0.0757
-0.0947
refined
19.2960
78.5452
27.1236
X-RAY DIFFRACTION
2.9919
1.5443
-2.4187
4.5978
-2.2967
4.9265
-0.0930
-0.0827
0.0972
0.1565
0.0308
0.1339
0.2259
-0.3391
0.0622
0.0123
-0.0268
0.0039
0.0088
-0.0152
-0.0353
refined
22.3750
72.9649
39.6628
X-RAY DIFFRACTION
3.7286
-1.5147
0.0920
1.6663
0.2696
0.7421
0.2961
0.1797
0.1402
-0.4440
-0.2409
-0.1179
0.3113
-0.1436
-0.0552
0.2185
-0.0196
0.1473
-0.0902
-0.0095
-0.0867
refined
36.5658
63.0713
26.8708
X-RAY DIFFRACTION
2.4266
0.6897
-0.4104
3.9158
0.1590
1.8175
0.1276
-0.0452
0.0343
0.0263
0.0868
0.1446
-0.0776
-0.0887
-0.2144
0.0163
0.0281
0.0464
-0.0564
-0.0088
-0.0097
refined
44.1169
44.9327
36.3526
X-RAY DIFFRACTION
A
11
A
4
A
29
A
22
X-RAY DIFFRACTION
1
ALL
A
30
A
23
A
125
A
118
X-RAY DIFFRACTION
2
ALL
A
126
A
119
A
197
A
190
X-RAY DIFFRACTION
3
ALL
A
198
A
191
A
306
A
299
X-RAY DIFFRACTION
4
ALL
author_defined_assembly
1
monomeric
A
MSE
101
SELENOMETHIONINE
A
MSE
94
MET
A
MSE
191
SELENOMETHIONINE
A
MSE
184
MET
A
MSE
295
SELENOMETHIONINE
A
MSE
288
MET
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
A
N
LEU
60
A
N
LEU
53
A
O
ILE
94
A
O
ILE
87
A
N
VAL
93
A
N
VAL
86
A
O
VAL
123
A
O
VAL
116
A
O
LEU
124
A
O
LEU
117
A
N
ILE
28
A
N
ILE
21
A
N
ASN
31
A
N
ASN
24
A
O
VAL
143
A
O
VAL
136
1
A
CD
ARG
18
A
CD
ARG
11
1
Y
1
A
NE
ARG
18
A
NE
ARG
11
1
Y
1
A
CZ
ARG
18
A
CZ
ARG
11
1
Y
1
A
NH1
ARG
18
A
NH1
ARG
11
1
Y
1
A
NH2
ARG
18
A
NH2
ARG
11
1
Y
1
A
CG
GLU
33
A
CG
GLU
26
1
Y
1
A
CD
GLU
33
A
CD
GLU
26
1
Y
1
A
OE1
GLU
33
A
OE1
GLU
26
1
Y
1
A
OE2
GLU
33
A
OE2
GLU
26
1
Y
1
A
CE
LYS
55
A
CE
LYS
48
1
Y
1
A
NZ
LYS
55
A
NZ
LYS
48
1
Y
1
A
CG
GLU
67
A
CG
GLU
60
1
Y
1
A
CD
GLU
67
A
CD
GLU
60
1
Y
1
A
OE1
GLU
67
A
OE1
GLU
60
1
Y
1
A
OE2
GLU
67
A
OE2
GLU
60
1
Y
1
A
OD1
ASP
79
A
OD1
ASP
72
1
Y
1
A
OD2
ASP
79
A
OD2
ASP
72
1
Y
1
A
CG
LYS
111
A
CG
LYS
104
1
Y
1
A
CD
LYS
111
A
CD
LYS
104
1
Y
1
A
CE
LYS
111
A
CE
LYS
104
1
Y
1
A
NZ
LYS
111
A
NZ
LYS
104
1
Y
1
A
CB
GLU
115
A
CB
GLU
108
1
Y
1
A
CG
GLU
115
A
CG
GLU
108
1
Y
1
A
CD
GLU
115
A
CD
GLU
108
1
Y
1
A
OE1
GLU
115
A
OE1
GLU
108
1
Y
1
A
OE2
GLU
115
A
OE2
GLU
108
1
Y
1
A
CD1
LEU
133
A
CD1
LEU
126
1
Y
1
A
CD2
LEU
133
A
CD2
LEU
126
1
Y
1
A
CE
LYS
137
A
CE
LYS
130
1
Y
1
A
NZ
LYS
137
A
NZ
LYS
130
1
Y
1
A
CG1
VAL
144
A
CG1
VAL
137
1
Y
1
A
CG2
VAL
144
A
CG2
VAL
137
1
Y
1
A
CG
LYS
149
A
CG
LYS
142
1
Y
1
A
CD
LYS
149
A
CD
LYS
142
1
Y
1
A
CE
LYS
149
A
CE
LYS
142
1
Y
1
A
NZ
LYS
149
A
NZ
LYS
142
1
Y
1
A
CG
GLU
157
A
CG
GLU
150
1
Y
1
A
CD
GLU
157
A
CD
GLU
150
1
Y
1
A
OE1
GLU
157
A
OE1
GLU
150
1
Y
1
A
OE2
GLU
157
A
OE2
GLU
150
1
Y
1
A
CE
LYS
158
A
CE
LYS
151
1
Y
1
A
NZ
LYS
158
A
NZ
LYS
151
1
Y
1
A
NZ
LYS
181
A
NZ
LYS
174
1
Y
1
A
CG
GLU
185
A
CG
GLU
178
1
Y
1
A
CD
GLU
185
A
CD
GLU
178
1
Y
1
A
OE1
GLU
185
A
OE1
GLU
178
1
Y
1
A
OE2
GLU
185
A
OE2
GLU
178
1
Y
1
A
CD
GLU
198
A
CD
GLU
191
1
Y
1
A
OE1
GLU
198
A
OE1
GLU
191
1
Y
1
A
OE2
GLU
198
A
OE2
GLU
191
1
Y
1
A
CD
GLU
200
A
CD
GLU
193
1
Y
1
A
OE1
GLU
200
A
OE1
GLU
193
1
Y
1
A
OE2
GLU
200
A
OE2
GLU
193
1
Y
1
A
CE
LYS
201
A
CE
LYS
194
1
Y
1
A
NZ
LYS
201
A
NZ
LYS
194
1
Y
1
A
CG
LYS
209
A
CG
LYS
202
1
Y
1
A
CD
LYS
209
A
CD
LYS
202
1
Y
1
A
CE
LYS
209
A
CE
LYS
202
1
Y
1
A
NZ
LYS
209
A
NZ
LYS
202
1
Y
1
A
CG
LYS
246
A
CG
LYS
239
1
Y
1
A
CD
LYS
246
A
CD
LYS
239
1
Y
1
A
CE
LYS
246
A
CE
LYS
239
1
Y
1
A
NZ
LYS
246
A
NZ
LYS
239
1
Y
1
A
NH1
ARG
257
A
NH1
ARG
250
1
Y
1
A
NH2
ARG
257
A
NH2
ARG
250
1
Y
1
A
CB
GLU
266
A
CB
GLU
259
1
Y
1
A
CG
GLU
266
A
CG
GLU
259
1
Y
1
A
CD
GLU
266
A
CD
GLU
259
1
Y
1
A
OE1
GLU
266
A
OE1
GLU
259
1
Y
1
A
OE2
GLU
266
A
OE2
GLU
259
1
Y
1
A
CB
SER
267
A
CB
SER
260
1
Y
1
A
OG
SER
267
A
OG
SER
260
1
Y
1
A
CZ
ARG
282
A
CZ
ARG
275
1
Y
1
A
NH1
ARG
282
A
NH1
ARG
275
1
Y
1
A
NH2
ARG
282
A
NH2
ARG
275
1
Y
1
A
CD
LYS
284
A
CD
LYS
277
1
Y
1
A
CE
LYS
284
A
CE
LYS
277
1
Y
1
A
NZ
LYS
284
A
NZ
LYS
277
1
Y
1
A
CZ
ARG
304
A
CZ
ARG
297
1
Y
1
A
NH1
ARG
304
A
NH1
ARG
297
1
Y
1
A
NH2
ARG
304
A
NH2
ARG
297
1
Y
1
A
GLY
8
A
GLY
1
1
Y
1
A
ALA
9
A
ALA
2
1
Y
1
A
LYS
10
A
LYS
3
1
Y
1
A
GLY
307
A
GLY
300
1
Y
1
A
VAL
308
A
VAL
301
1
Y
1
A
ASN
309
A
ASN
302
1
Y
1
A
ALA
310
A
ALA
303
1
Y
1
A
TRP
311
A
TRP
304
1
Y
1
A
SER
312
A
SER
305
1
Y
1
A
GLU
24
-115.54
61.37
1
A
ASP
63
-160.53
75.88
34.573
-0.960
0.000
0.000
-0.960
0.000
1.910
0.943
0.907
1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3). TWO MOLECULES OF 2-ETHOXYETHANOL FROM THE CRYSTALLIZATION BUFFER HAS BEEN MODELED INTO THE STRUCTURE. 4). AN UNKNOWN LIGAND HAS BEEN MODELED INTO THE STRUCTURE BETWEEN THE SIDECHAINS OF LEU 168 AND ARG 254. 5.) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
0.278
0.22
0.223
2.000
27.94
1130
22103
5.100
99.260
10.889
0.153
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.217
0.197
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
2.000
27.94
107
2470
17
0
2346
0.013
0.022
2466
0.003
0.020
2343
1.684
1.989
3341
1.188
3.000
5432
2.099
5.000
309
25.182
24.112
107
8.319
15.000
458
8.252
15.000
18
0.107
0.200
387
0.006
0.020
2707
0.002
0.020
487
0.180
0.300
532
0.123
0.300
2275
0.165
0.500
1206
0.081
0.500
1307
0.169
0.500
174
0.145
0.300
11
0.109
0.300
55
0.220
0.500
17
1.427
3.000
1513
0.385
3.000
605
2.420
5.000
2458
4.208
8.000
977
6.140
11.000
881
0.306
0.257
2.053
95
1504
1599
20
99.130
42.314
2.000
27.9
2GNO
22105
0.041
1
11.880
94.700
0.415
2.00
2.07
2.0
6860
3580
1
83.80
0.314
2.07
2.15
2.7
7034
3711
1
90.10
0.251
2.15
2.25
3.3
7757
4060
1
92.20
0.184
2.25
2.37
4.5
7788
4072
1
93.60
0.125
2.37
2.52
6.3
7968
4166
1
97.00
0.093
2.52
2.71
8.3
7792
4088
1
97.80
0.067
2.71
2.99
10.9
8351
4353
1
98.70
0.046
2.99
3.42
15.5
8021
4231
1
99.70
0.025
3.42
25.1
7896
4199
1
99.10
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran
http://www.ccp4.ac.uk/main.html
REFMAC
5.2.0005
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html
XSCALE
data extraction
PDB
sw-help@rcsb.rutgers.edu
Nov. 1, 2005
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
1.701
data reduction
XDS
phasing
SHARP
V. 1
Crystal structure of a dna polymerase iii, gamma subunit-related protein (tm0771) from thermotoga maritima msb8 at 2.00 A resolution
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
A
ASP
11
A
ASP
4
HELX_P
A
LYS
22
A
LYS
15
1
1
12
A
SER
36
A
SER
29
HELX_P
A
LYS
51
A
LYS
44
1
2
16
A
GLY
70
A
GLY
63
HELX_P
A
ASN
82
A
ASN
75
1
3
13
A
ASP
97
A
ASP
90
HELX_P
A
MSE
101
A
MSE
94
5
4
5
A
THR
102
A
THR
95
HELX_P
A
PHE
109
A
PHE
102
1
5
8
A
PHE
109
A
PHE
102
HELX_P
A
GLU
115
A
GLU
108
1
6
7
A
ARG
128
A
ARG
121
HELX_P
A
LEU
132
A
LEU
125
5
7
5
A
LEU
133
A
LEU
126
HELX_P
A
SER
138
A
SER
131
1
8
6
A
PRO
148
A
PRO
141
HELX_P
A
GLY
160
A
GLY
153
1
9
13
A
ASP
161
A
ASP
154
HELX_P
A
LEU
166
A
LEU
159
1
10
6
A
PRO
167
A
PRO
160
HELX_P
A
ARG
171
A
ARG
164
5
11
5
A
ASP
172
A
ASP
165
HELX_P
A
LEU
197
A
LEU
190
1
12
26
A
GLU
198
A
GLU
191
HELX_P
A
LEU
203
A
LEU
196
1
13
6
A
LYS
209
A
LYS
202
HELX_P
A
VAL
227
A
VAL
220
1
14
19
A
GLU
228
A
GLU
221
HELX_P
A
LYS
230
A
LYS
223
5
15
3
A
GLU
231
A
GLU
224
HELX_P
A
ILE
243
A
ILE
236
1
16
13
A
GLY
245
A
GLY
238
HELX_P
A
GLU
262
A
GLU
255
1
17
18
A
SER
267
A
SER
260
HELX_P
A
ARG
282
A
ARG
275
1
18
16
A
VAL
283
A
VAL
276
HELX_P
A
LEU
288
A
LEU
281
5
19
6
A
ASN
289
A
ASN
282
HELX_P
A
ARG
306
A
ARG
299
1
20
18
covale
1.341
both
A
ARG
100
A
C
ARG
93
1_555
A
MSE
101
A
N
MSE
94
1_555
covale
1.331
both
A
MSE
101
A
C
MSE
94
1_555
A
THR
102
A
N
THR
95
1_555
covale
1.329
both
A
LEU
190
A
C
LEU
183
1_555
A
MSE
191
A
N
MSE
184
1_555
covale
1.337
both
B
A
MSE
191
A
C
MSE
184
1_555
A
GLU
192
A
N
GLU
185
1_555
covale
1.334
both
A
A
MSE
191
A
C
MSE
184
1_555
A
GLU
192
A
N
GLU
185
1_555
covale
1.330
both
A
LEU
294
A
C
LEU
287
1_555
A
MSE
295
A
N
MSE
288
1_555
covale
1.328
both
A
MSE
295
A
C
MSE
288
1_555
A
ASN
296
A
N
ASN
289
1_555
REPLICATION
Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, replication
Q9WZM9_THEMA
UNP
1
9
Q9WZM9
9
312
2GNO
9
312
Q9WZM9
A
1
2
305
1
expression tag
GLY
8
2GNO
A
Q9WZM9
UNP
1
1
MET
modified residue
MSE
101
2GNO
A
Q9WZM9
UNP
101
94
1
MET
modified residue
MSE
191
2GNO
A
Q9WZM9
UNP
191
184
1
MET
modified residue
MSE
295
2GNO
A
Q9WZM9
UNP
295
288
5
parallel
parallel
parallel
parallel
A
VAL
59
A
VAL
52
A
ILE
62
A
ILE
55
A
LYS
91
A
LYS
84
A
VAL
95
A
VAL
88
A
ALA
120
A
ALA
113
A
THR
126
A
THR
119
A
ILE
26
A
ILE
19
A
ASN
31
A
ASN
24
A
PHE
141
A
PHE
134
A
VAL
144
A
VAL
137
BINDING SITE FOR RESIDUE UNL A 1
A
UNL
1
Software
5
BINDING SITE FOR RESIDUE ETX A 3
A
ETX
3
Software
3
BINDING SITE FOR RESIDUE ETX A 4
A
ETX
4
Software
4
A
LEU
168
A
LEU
161
5
1_555
A
ASP
172
A
ASP
165
5
1_555
A
GLY
210
A
GLY
203
5
1_555
A
TYR
214
A
TYR
207
5
1_555
A
ARG
254
A
ARG
247
5
1_555
A
GLU
219
A
GLU
212
3
1_555
A
ARG
223
A
ARG
216
3
1_555
A
VAL
227
A
VAL
220
3
1_555
A
LEU
43
A
LEU
36
4
1_555
A
PRO
54
A
PRO
47
4
1_555
A
VAL
59
A
VAL
52
4
1_555
A
LYS
230
A
LYS
223
4
4_565
79
I 4