SASDDL3: Folded ribonuclease A (RNAse) (Ribonuclease pancreatic, RNase)

基本情報

• 登録情報: データベース: SASBDB / ID: SASDDL3

試料

Folded ribonuclease A (RNAse)

• Ribonuclease pancreatic (protein), RNase, Bos taurus

機能・相同性

分子機能:

pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region

ドメイン・相同性:

Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease

構成要素:

Ribonuclease pancreatic

• 生物種: Bos taurus (ウシ)
• 引用: ジャーナル: Biophys J / 年: 2018; タイトル: Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions.; 著者: Daniel Franke / Cy M Jeffries / Dmitri I Svergun / ; 要旨: Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vectors and how a simple k-nearest neighbor approach is able to retrieve information on overall particle shape and maximal diameter (D) as well as molecular mass directly from experimental scattering data. Based on this transformation, we develop a rapid multiclass shape-classification ranging from compact, extended, and flat categories to hollow and random-chain-like objects. This classification may be employed, e.g., as a decision block in automated data analysis pipelines. Further, we map protein structures from the Protein Data Bank into the classification space and, in a second step, use this mapping as a data source to obtain accurate estimates for the structural parameters (D, molecular mass) of the macromolecule under study based on the experimental scattering pattern alone, without inverse Fourier transform for D. All methods presented are implemented in a Fortran binary DATCLASS, part of the ATSAS data analysis suite, available on Linux, Mac, and Windows and free for academic use.

登録者

• Cy M Jeffries (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

モデル

• モデル #1787: ; タイプ: atomic / ソフトウェア: (PDB) / ダミー原子の半径: 1.90 A / 対称性: P1 / カイ2乗値: 0.821 / P-value: 0.174444; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: Folded ribonuclease A (RNAse) / 試料濃度: 5.24 mg/ml
• バッファ: 名称: phosphate buffered saline (PBS) / pH: 7

要素 #17

名称: RNase / タイプ: protein / 記述: Ribonuclease pancreatic / 分子量: 16.46 / 分子数: 1 / 由来: Bos taurus / 参照: UniProt: P61823
配列:

MALKSLVLLS LLVLVLLLVR VQPSLGKETA AAKFERQHMD SSTSAASSSN YCNQMMKSRN LTKDRCKPVN TFVHESLADV QAVCSQKNVA CKNGQTNCYQ SYSTMSITDC RETGSSKYPN CAYKTTQANK HIIVACEGNP YVPVHFDASV

実験情報

• ビーム: 設備名称: PETRA III EMBL P12 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotron / 波長: 0.124 Å / スペクトロメータ・検出器間距離: 3.1 mm
• 検出器: 名称: Pilatus 2M

スキャン

タイトル: Folded ribonuclease A (RNAse) / 測定日: 2013年7月29日 / 保管温度: 10 °C / セル温度: 10 °C / 照射時間: 0.05 sec. / フレーム数: 2 / 単位: 1/nm /

	Min	Max
Q	0.0536	3.4949

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.6 / ポイント数: 427 /

	Min	Max
Q	0.08254	3.488
P(R) point	14	440
R	0	5.56

結果

カーブのタイプ: single_conc

	実験値	Standard	Porod
分子量	17.4 kDa	17.4 kDa	10 kDa
体積	-	-	15.9 nm3

	P(R)	Guinier	Guinier error
前方散乱 I0	626.3	629.71	2.21
慣性半径, Rg	1.61 nm	1.61 nm	0.06

	Min	Max
D	-	5.56
Guinier point	22	379