- PDB-2f22: CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTE... -
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基本情報
登録情報
データベース: PDB / ID: 2f22
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTEIN (BH3987) FROM BACILLUS HALODURANS AT 1.42 A RESOLUTION
要素
BH3987
キーワード
METAL BINDING PROTEIN / PUTATIVE DNA DAMAGE-INDUCABLE (DINB) PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
DNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICKEL (II) ION / Unknown
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
解像度: 1.35→24.3 Å / Num. obs: 58327 / % possible obs: 98.9 % / 冗長度: 4.8 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 5.9
反射 シェル
Diffraction-ID: 1
解像度 (Å)
% possible obs (%)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Rsym value
1.42-1.46
91.8
2.9
0.484
1.5
3941
0.484
1.46-1.5
95.8
3.2
0.385
1.9
4047
0.385
1.5-1.54
98.1
3.5
0.326
2.1
3963
0.326
1.54-1.59
100
3.6
0.287
2.5
3993
0.287
1.59-1.64
100
3.6
0.248
3
3839
0.248
1.64-1.7
100
3.6
0.213
3.4
3749
0.213
1.7-1.76
100
3.6
0.191
3.8
3586
0.191
1.76-1.83
100
3.6
0.16
4.4
3485
0.16
1.83-1.91
100
3.6
0.139
5
3332
0.139
1.91-2.01
100
3.6
0.12
5.5
3203
0.12
2.01-2.12
100
6.7
0.138
5
3033
0.138
2.12-2.25
100
7.2
0.122
5.6
2915
0.122
2.25-2.4
99.9
7.3
0.108
6.4
2693
0.108
2.4-2.59
100
7.2
0.093
7.4
2564
0.093
2.59-2.84
100
7.2
0.083
8.3
2333
0.083
2.84-3.18
99.9
7.1
0.075
8.7
2140
0.075
3.18-3.67
99.8
7.1
0.066
9.8
1891
0.066
3.67-4.49
99.6
6.9
0.059
10.7
1633
0.059
4.49-6.35
99.4
6.7
0.065
9.6
1266
0.065
6.35-24.3
96.2
5.9
0.069
8.6
721
0.069
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
SCALA
データスケーリング
PDB_EXTRACT
1.601
データ抽出
MOSFLM
データ削減
CCP4
(SCALA)
データスケーリング
SOLVE
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.42→23.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.778 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 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 ...詳細: 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. NI ATOMS MODELED BASED ON ANOMALOUS AND DIFFERENCE MAPS.
Rfactor
反射数
%反射
Selection details
Rfree
0.182
2955
5.1 %
RANDOM
Rwork
0.157
-
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all
0.158
-
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obs
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55316
98.65 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK