ジャーナル: To be published タイトル: Crystal structure of hypothetical protein (JCVI_PEP_1096665735785) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 1.70 A resolution 著者: Joint Center for Structural Genomics (JCSG)
BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE (1) 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. (2) THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN THE UNP DATABASE AT THE TIME OF PROCESSING. (3) PRODUCT OF THE EXPRESSED SYNTHETIC GENE WAS BASED ON THE PREDICTED SEQUENCE OF ACCESSION ID JCVI_PEP_1096665735785 FROM THE J. CRAIG VENTER INSTITUTE.
SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
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要素
#1: タンパク質
hypotheticalprotein /
分子量: 11721.772 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) uncultured marine organism (環境試料) 解説: SYNTHETIC GENE: The gene product was based on JCVI_PEP_1096665735785 from the Sorcerer II Global Ocean Sampling experiment 発現宿主: Escherichia coli (大腸菌)
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
0.97966
1
反射
解像度: 1.7→28.892 Å / Num. obs: 22797 / % possible obs: 98.3 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 6.76
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Diffraction-ID
% possible all
1.7-1.76
0.403
2.02
7045
1
99
1.76-1.83
0.337
2.47
7002
1
98.9
1.83-1.91
0.257
3.07
6894
1
98.4
1.91-2.02
0.175
4.27
7704
1
98.6
2.02-2.14
0.125
5.55
6687
1
99
2.14-2.31
0.091
6.89
7288
1
98.5
2.31-2.54
0.075
8.06
6984
1
98.3
2.54-2.9
0.063
9.66
7006
1
97.9
2.9-3.66
0.05
12.1
7195
1
97.5
3.66-28.9
0.04
13.73
7089
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
MolProbity
3beta29
モデル構築
SOLVE
位相決定
REFMAC
5.2.0019
精密化
XSCALE
データスケーリング
PDB_EXTRACT
2
データ抽出
Blu-Ice
V. 5.0
データ収集
XDS
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→28.892 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.644 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.098 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. AN EDO MOLECULE FROM THE CRYO SOLUTION IS MODELED. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
Rfactor
反射数
%反射
Selection details
Rfree
0.193
1172
5.1 %
RANDOM
Rwork
0.159
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-
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obs
0.161
22774
99.11 %
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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