- PDB-8iud: Crystal Structure of bacterial defense protein GajB -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 8iud
Title
Crystal Structure of bacterial defense protein GajB
Components
Gabija protein GajB
Keywords
UNKNOWN FUNCTION / bacterial antiphage defense system / Gabija / GajB
Function / homology
Function and homology information
recombinational repair / 3'-5' DNA helicase activity / defense response to virus / hydrolase activity / DNA binding / ATP binding Similarity search - Function
Method to determine structure: SAD / Resolution: 2→28.468 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.17 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2335
3779
4.14 %
Rwork
0.197
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-
obs
0.1986
91384
99.17 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2→28.468 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3873
0
0
265
4138
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
3937
X-RAY DIFFRACTION
f_angle_d
0.953
5310
X-RAY DIFFRACTION
f_dihedral_angle_d
12.405
1487
X-RAY DIFFRACTION
f_chiral_restr
0.042
604
X-RAY DIFFRACTION
f_plane_restr
0.004
682
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2-2.0243
0.3288
117
0.3038
2892
X-RAY DIFFRACTION
88
2.0243-2.051
0.355
151
0.292
3263
X-RAY DIFFRACTION
100
2.051-2.079
0.3206
118
0.2851
3318
X-RAY DIFFRACTION
100
2.079-2.1087
0.3141
143
0.2586
3231
X-RAY DIFFRACTION
100
2.1087-2.1402
0.3333
143
0.2556
3310
X-RAY DIFFRACTION
100
2.1402-2.1736
0.29
146
0.2443
3244
X-RAY DIFFRACTION
100
2.1736-2.2093
0.2785
134
0.2388
3282
X-RAY DIFFRACTION
100
2.2093-2.2473
0.2688
143
0.2332
3246
X-RAY DIFFRACTION
100
2.2473-2.2882
0.2705
141
0.2355
3310
X-RAY DIFFRACTION
100
2.2882-2.3322
0.2747
135
0.2175
3267
X-RAY DIFFRACTION
100
2.3322-2.3798
0.2689
142
0.2319
3258
X-RAY DIFFRACTION
100
2.3798-2.4315
0.2881
127
0.2221
3250
X-RAY DIFFRACTION
100
2.4315-2.488
0.3138
148
0.2204
3254
X-RAY DIFFRACTION
100
2.488-2.5502
0.2834
136
0.2123
3280
X-RAY DIFFRACTION
100
2.5502-2.6191
0.2253
140
0.2031
3275
X-RAY DIFFRACTION
100
2.6191-2.6961
0.28
144
0.1964
3282
X-RAY DIFFRACTION
100
2.6961-2.783
0.2058
148
0.2086
3229
X-RAY DIFFRACTION
100
2.783-2.8824
0.293
150
0.2292
3285
X-RAY DIFFRACTION
100
2.8824-2.9977
0.2663
128
0.2197
3268
X-RAY DIFFRACTION
100
2.9977-3.134
0.2328
148
0.2174
3239
X-RAY DIFFRACTION
100
3.134-3.299
0.2771
146
0.2072
3261
X-RAY DIFFRACTION
100
3.299-3.5053
0.2037
138
0.1949
3294
X-RAY DIFFRACTION
100
3.5053-3.7754
0.1733
143
0.1664
3246
X-RAY DIFFRACTION
100
3.7754-4.1543
0.1845
140
0.1616
3265
X-RAY DIFFRACTION
100
4.1543-4.753
0.1565
146
0.1398
3256
X-RAY DIFFRACTION
99
4.753-5.9792
0.2049
152
0.1794
3235
X-RAY DIFFRACTION
100
5.9792-28.468
0.2802
132
0.1993
3065
X-RAY DIFFRACTION
94
Refinement TLS params.
Method: refined / Origin x: 32.474 Å / Origin y: 60.4742 Å / Origin z: 61.3164 Å
11
12
13
21
22
23
31
32
33
T
0.3508 Å2
0.0154 Å2
0.0298 Å2
-
0.2592 Å2
-0.0078 Å2
-
-
0.2536 Å2
L
0.3969 °2
0.3309 °2
0.3247 °2
-
0.6149 °2
0.1754 °2
-
-
0.6657 °2
S
-0.0452 Å °
-0.0012 Å °
-0.0274 Å °
-0.0039 Å °
0.0396 Å °
-0.0319 Å °
0.0171 Å °
0.0013 Å °
0.0063 Å °
Refinement TLS group
Selection details: all
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