- PDB-4lba: Crystal structure of a conjugative transposon lipoprotein (BACEGG... -
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基本情報
登録情報
データベース: PDB / ID: 4lba
タイトル
Crystal structure of a conjugative transposon lipoprotein (BACEGG_03088) from Bacteroides eggerthii DSM 20697 at 1.70 A resolution
要素
conjugative transposon lipoprotein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12988 family protein / DUF3872 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 32-167 OF THE TARGET SEQUENCE.
モノクロメーター: single crystal Si(111) bent / 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
0.97864
1
3
0.97817
1
反射
解像度: 1.7→25.217 Å / Num. all: 40202 / Num. obs: 40202 / % possible obs: 99.8 % / 冗長度: 6.2 % / Rsym value: 0.08 / Net I/σ(I): 12.6
反射 シェル
Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.7-1.74
6
0.828
0.9
17712
2954
0.828
100
1.74-1.79
6.4
0.635
1.2
18612
2893
0.635
100
1.79-1.84
6.4
0.496
1.6
18009
2800
0.496
99.9
1.84-1.9
6.2
0.366
2.1
16751
2703
0.366
100
1.9-1.96
6
0.267
2.8
15928
2641
0.267
100
1.96-2.03
5.5
0.206
3.5
13983
2523
0.206
99.5
2.03-2.11
5.9
0.169
4.4
14504
2478
0.169
99.9
2.11-2.19
6.5
0.143
5.2
15507
2388
0.143
100
2.19-2.29
6.5
0.122
6.1
14688
2265
0.122
100
2.29-2.4
6.4
0.11
6.5
13816
2175
0.11
99.9
2.4-2.53
6.2
0.094
7.5
12858
2059
0.094
99.8
2.53-2.69
5.3
0.078
8.9
10514
1968
0.078
99.5
2.69-2.87
6.7
0.071
9.4
12521
1867
0.071
100
2.87-3.1
6.6
0.064
9.5
11353
1727
0.064
100
3.1-3.4
6.4
0.06
9.2
10207
1592
0.06
100
3.4-3.8
5.6
0.057
8.6
8026
1438
0.057
99.1
3.8-4.39
6
0.059
8.8
7836
1297
0.059
99.6
4.39-5.38
6.4
0.058
9.7
6984
1088
0.058
100
5.38-7.6
5.4
0.066
7.5
4600
857
0.066
99.9
7.6-25.217
6.4
0.05
11.4
3113
489
0.05
97.4
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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
MolProbity
3beta29
モデル構築
PDB_EXTRACT
3.1
データ抽出
SOLVE
位相決定
SCALA
3.3.20
データスケーリング
REFMAC
精密化
MOSFLM
データ削減
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.7→25.217 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 3.06 / SU ML: 0.051 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077 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. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. PEG3350 FRAGMENT (1PE) AND 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.1873
2012
5 %
RANDOM
Rwork
0.1651
-
-
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obs
0.1662
40187
99.8 %
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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: BABINET MODEL WITH MASK