- PDB-3i7d: Crystal structure of sugar phosphate isomerase from a cupin super... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 3i7d
タイトル
Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi (YP_168127.1) from SILICIBACTER POMEROYI DSS-3 at 2.30 A resolution
要素
sugar phosphate isomerase
キーワード
ISOMERASE / YP_168127.1 / sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / sugar metabolism
機能・相同性
機能・相同性情報
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta 類似検索 - ドメイン・相同性
ACETATE ION / CACODYLATE ION / DI(HYDROXYETHYL)ETHER / Cupin_2 domain-containing protein 類似検索 - 構成要素
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.
解像度: 2.3→29.761 Å / Num. obs: 16869 / % possible obs: 99.9 % / 冗長度: 9.3 % / Biso Wilson estimate: 23.149 Å2 / Rmerge(I) obs: 0.336 / Rsym value: 0.336 / Net I/σ(I): 8.3
反射 シェル
Rmerge(I) obs: 0.012 / Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.3-2.36
9.5
0.6
11235
1188
1.204
99.7
2.36-2.42
9.6
0.7
11316
1182
1.094
99.8
2.42-2.49
9.5
0.7
10911
1147
1.038
99.8
2.49-2.57
9.5
0.8
10601
1113
0.975
99.8
2.57-2.66
9.4
0.9
10263
1095
0.825
100
2.66-2.75
9.5
1
10005
1052
0.731
100
2.75-2.85
9.4
1.3
9440
1002
0.609
100
2.85-2.97
9.4
1.5
9436
1004
0.497
99.9
2.97-3.1
9.4
1.8
8990
955
0.416
100
3.1-3.25
9.4
2.2
8360
892
0.341
99.9
3.25-3.43
9.3
3
8064
871
0.255
99.9
3.43-3.64
9.3
3.9
7629
819
0.195
99.9
3.64-3.89
9.2
4.1
7309
794
0.184
99.9
3.89-4.2
9.2
5.3
6744
734
0.14
100
4.2-4.6
9.1
6.4
6170
679
0.116
99.9
4.6-5.14
8.9
6.4
5683
635
0.115
100
5.14-5.94
8.7
4.8
5023
577
0.155
100
5.94-7.27
8.6
4.4
4143
483
0.169
100
7.27-10.29
8.1
6
3299
405
0.125
100
10.29-29.76
6.9
8.9
1672
242
0.08
95.3
-
位相決定
位相決定
手法: 多波長異常分散
-
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
SCALA
3.2.5
データスケーリング
PDB_EXTRACT
3.006
データ抽出
MOSFLM
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→29.761 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 7.302 / SU ML: 0.173 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.23 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. CHLORIDE (CL), CACODYLATE (CAC) AND ACETATE (ACT) IONS, AND PEG8000 FRAGMENT(PEG) MOLECULES ARE MODELED BASED ON CRYSTALLIZATION CONDITION.
Rfactor
反射数
%反射
Selection details
Rfree
0.245
850
5.1 %
RANDOM
Rwork
0.196
-
-
-
obs
0.198
16826
99.75 %
-
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