- PDB-3dka: Crystal structure of a dinb-like protein (yjoa, bsu12410) from ba... -
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IDまたはキーワード:
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基本情報
登録情報
データベース: PDB / ID: 3dka
タイトル
Crystal structure of a dinb-like protein (yjoa, bsu12410) from bacillus subtilis at 2.30 A resolution
要素
DinB-like Protein
キーワード
UNKNOWN FUNCTION / Dinb/yfit-like putative metalloenzyme fold / 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 / metal ion binding / Uncharacterized protein YjoA
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.
モノクロメーター: Single crystal Si(111) bent monochromator (horizontal focusing) プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.91837
1
2
0.97956
1
3
0.97904
1
反射
解像度: 2.3→29.566 Å / Num. obs: 13596 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / 冗長度: 3.63 % / Biso Wilson estimate: 34.972 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.3
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.3-2.38
0.571
1.58
4548
2313
1
90.5
2.38-2.48
0.462
1.9
5203
2619
1
96.1
2.48-2.59
0.378
2.4
4812
2441
1
96.4
2.59-2.73
0.28
3
5069
2554
1
96
2.73-2.9
0.214
3.9
4885
2460
1
96
2.9-3.12
0.163
5
4873
2468
1
97.2
3.12-3.43
0.107
7.6
4973
2501
1
96.8
3.43-3.93
0.06
12
4994
2523
1
96.4
3.93-4.93
0.04
16.6
4955
2499
1
97.1
4.93-29.57
0.035
18.5
5051
2562
1
96.5
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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
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3.004
データ抽出
XDS
データ削減
SHELXD
位相決定
autoSHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.3→29.566 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 15.654 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.273 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
Rfactor
反射数
%反射
Selection details
Rfree
0.269
677
5 %
RANDOM
Rwork
0.217
-
-
-
obs
0.219
13568
97.56 %
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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