- PDB-3u21: Crystal structure of a Fragment of Nuclear factor related to kapp... -
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基本情報
登録情報
データベース: PDB / ID: 3u21
タイトル
Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution
要素
Nuclear factor related to kappa-B-binding protein
キーワード
Transcription regulation / DNA BINDING / DNA/RNA-binding 3-helical bundle / winged-HTH domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / DNA BINDING PROTEIN / Partnership for Stem Cell Biology / STEMCELL
機能・相同性
機能・相同性情報
regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / Ino80 complex / regulation of chromosome organization / regulation of DNA replication / regulation of embryonic development / regulation of DNA repair / positive regulation of DNA repair / telomere maintenance / DNA Damage Recognition in GG-NER ...regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / Ino80 complex / regulation of chromosome organization / regulation of DNA replication / regulation of embryonic development / regulation of DNA repair / positive regulation of DNA repair / telomere maintenance / DNA Damage Recognition in GG-NER / UCH proteinases / protease binding / DNA recombination / regulation of cell cycle / chromatin remodeling / DNA repair / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus 類似検索 - 分子機能
1. THIS CONSTRUCT (RESIDUES 370-495) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THIS CONSTRUCT (RESIDUES 370-495) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. RESIDUE NUMBERING IS BASED ON ISOFORM 1 OF UNIPROTKB ID Q6P4R8. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
解像度: 2.18→35.466 Å / Num. obs: 13560 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.259 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.78
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
2.18-2.26
0.796
2.4
9710
1360
99.9
2.26-2.35
0.624
3.1
9264
1298
99.8
2.35-2.45
0.506
3.8
8939
1247
100
2.45-2.58
0.365
5.3
9488
1332
100
2.58-2.75
0.248
7.9
10006
1409
100
2.75-2.96
0.152
12.2
9368
1322
100
2.96-3.25
0.101
18.1
9300
1316
100
3.25-3.72
0.047
35.2
9515
1369
99.9
3.72-4.68
0.029
53.2
9606
1407
99.9
4.68
0.024
58.9
9421
1500
98.3
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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
SHELX
位相決定
SHARP
位相決定
XSCALE
December6, 2010
データスケーリング
REFMAC
5.6.0116
精密化
XDS
データ削減
SHELXD
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.18→35.466 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 12.518 / SU ML: 0.156 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.222 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 RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. SODIUM ION (NA) FROM CRYSTALLIZATION CONDITION WAS MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.2695
662
4.9 %
RANDOM
Rwork
0.2305
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-
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obs
0.2324
13504
99.75 %
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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