- PDB-3er7: Crystal structure of NTF2-like protein of unknown function (YP_00... -
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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: 3er7
タイトル
Crystal structure of NTF2-like protein of unknown function (YP_001812677.1) from EXIGUOBACTERIUM SP. 255-15 at 1.50 A resolution
要素
uncharacterized NTF2-like protein
キーワード
structural genomics / unknown function / YP_001812677.1 / NTF2-like protein of unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS FORMING A DIMER. CRYSTAL PACKING ANALYSIS SUGGESTS THAT THIS IS THE OLIGOMERIC FORM IN SOLUTION.
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.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 2.03 Å3/Da / 溶媒含有率: 39.37 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 詳細: 0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
解像度: 1.5→29.514 Å / Num. obs: 40169 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.153 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.44
反射 シェル
Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.55-1.61
0.425
1.9
13589
7230
97
1.61-1.67
0.321
2.4
11954
6320
99.6
1.67-1.75
0.254
3.1
13587
7175
99.3
1.75-1.84
0.174
4.4
12510
6583
99.2
1.84-1.95
0.105
7.2
12569
6574
99.1
1.95-2.1
0.068
10.6
13056
6811
99.1
2.1-2.31
0.047
14.6
13114
6820
98.8
2.31-2.65
0.037
18.4
13458
6975
99.2
2.65-3.33
0.024
26.7
13140
6776
99
3.33
0.019
34.9
13402
6859
98.2
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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
3.006
データ抽出
XDS
データ削減
SHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.5→29.514 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.82 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 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 RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.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. 4.CHLORIDE AND PEG (PEG3000 FRAGMENTS) FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.IT APPEARS PLAUSIBLE THAT A DISULFIDE BOND MAY FORM BETWEEN CYS87 RESIDUES IN CHAINS A AND B.
Rfactor
反射数
%反射
Selection details
Rfree
0.209
2014
5 %
RANDOM
Rwork
0.176
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obs
0.178
40122
99.68 %
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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