- PDB-2pbz: Crystal structure of an IMP biosynthesis protein PurP from Thermo... -
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基本情報
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データベース: PDB / ID: 2pbz
タイトル
Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis
要素
Hypothetical protein
キーワード
LIGASE / NYSGXRC / PSI-II / IMP biosynthesis / ATP binding protein / PurP / 10188d / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
機能・相同性
機能・相同性情報
IMP biosynthetic process / ligase activity, forming carbon-nitrogen bonds / magnesium ion binding / ATP binding 類似検索 - 分子機能
IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
モノクロメーター: SI(III) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.9792 Å / 相対比: 1
反射
解像度: 2.5→50 Å / Num. obs: 33174 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / 冗長度: 12 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5
反射 シェル
解像度: 2.5→2.59 Å / 冗長度: 5.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1 / % possible all: 68.1
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解析
ソフトウェア
名称
バージョン
分類
CNS
1.1
精密化
HKL-2000
データ削減
HKL-2000
データスケーリング
SHARP
位相決定
SHELXD
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.5→31 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 90726.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2 / 立体化学のターゲット値: ENGH & HUBER 詳細: 1. Restrained NCS was used during refinement due to paucity of data. 2. Residual density in the final difference map was modeled as ATP molecule. 3. Residues listed as missing in remark 465 ...詳細: 1. Restrained NCS was used during refinement due to paucity of data. 2. Residual density in the final difference map was modeled as ATP molecule. 3. Residues listed as missing in remark 465 were not modeled because of lack of electron density. 4. Outliers for Ramachandran plot were due to poor electron density except for His11 of all chains. The electron density for His 11 is well defined.