- PDB-4q9t: Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propel... -
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基本情報
登録情報
データベース: PDB / ID: 4q9t
タイトル
Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain
要素
Nucleoporin NUP133
キーワード
PROTEIN TRANSPORT / Nuclear Pore Complex / Nucleoporin / Nup84 complex / ALPS motif / Structural genomics / PSI-Biology / Nucleocytoplasmic Transport: a Target for Cellular Control / NPCXstals / New York SGX Research Center for Structural Genomics / NYSGXRC / Nup133 / Beta-propeller domain / and New York Structural Genomics Research Center / NYSGRC / Protein Structure Initiative / New York Structural Genomics Research Consortium
機能・相同性
機能・相同性情報
nuclear pore localization => GO:0051664 / mRNA export from nucleus in response to heat stress / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / subtelomeric heterochromatin formation ...nuclear pore localization => GO:0051664 / mRNA export from nucleus in response to heat stress / telomere tethering at nuclear periphery / nuclear pore outer ring / tRNA export from nucleus / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / subtelomeric heterochromatin formation / protein import into nucleus / double-strand break repair / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / membrane / cytosol 類似検索 - 分子機能
Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like 類似検索 - ドメイン・相同性
解像度: 3→3.18 Å / 冗長度: 13.9 % / Rmerge(I) obs: 0.02542 / Mean I/σ(I) obs: 1.2 / Num. unique all: 3224 / % possible all: 98.6
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.8.0049
精密化
PDB_EXTRACT
3.14
データ抽出
XDS
データ削減
XDS
データスケーリング
Aimless
データスケーリング
PHENIX
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 3→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 59.442 / SU ML: 0.439 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.461 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
反射数
%反射
Selection details
Rfree
0.2677
1042
5.1 %
RANDOM
Rwork
0.2149
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obs
0.2175
20310
99.42 %
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溶媒の処理
イオンプローブ半径: 0.9 Å / 減衰半径: 0.9 Å / VDWプローブ半径: 1 Å / 溶媒モデル: MASK