SASDDJ3: Candida antarctica lipase B - with guanidine-HCl unfolding series

Basic information

Entry

Database: SASBDB / ID: SASDDJ3

Sample

Candida antarctica lipase B - with guanidine-HCl unfolding series

• Lipase B from Pseudozyma antarctica (protein), lipase B, Pseudozyma antarctica (Candida antarctica)

• Function / homology: triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / Lipase B
• Biological species: Pseudozyma antarctica (Candida antarctica)
• Citation: Journal: Biophys J / Year: 2018; Title: Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions.; Authors: Daniel Franke / Cy M Jeffries / Dmitri I Svergun / ; Abstract: 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.

Contact author

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

Models

Sample

• Sample: Name: Candida antarctica lipase B - with guanidine-HCl unfolding series; Specimen concentration: 4.65 mg/ml
• Buffer: Name: 100 mM NaCl, 20 mM Na2HPO4 / pH: 6

Entity #968

Name: lipase B / Type: protein / Description: Lipase B from Pseudozyma antarctica / Formula weight: 33.022 / Source: Pseudozyma antarctica (Candida antarctica) / References: UniProt: P41365
Sequence:

LPSGSDPAFS QPKSVLDAGL TCQGASPSSV SKPILLVPGT GTTGPQSFDS NWIPLSTQLG YTPCWISPPP FMLNDTQVNT EYMVNAITAL YAGSGNNKLP VLTWSQGGLV AQWGLTFFPS IRSKVDRLMA FAPDYKGTVL AGPLDALAVS APSVWQQTTG SALTTALRNA GGLTQIVPTT NLYSATDEIV QPQVSNSPLD SSYLFNGKNV QAQAVCGPLF VIDHAGSLTS QFSYVVGRSA LRSTTGQARS ADYGITDCNP LPANDLTPEQ KVAAAALLAP AAAAIVAGPK QNCEPDLMPY ARPFAVGKRT CSGIVTP

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Candida antarctica lipase B - with guanidine-HCl unfolding series
Measurement date: Jul 29, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.03 sec. / Number of frames: 1 / Unit: 1/nm /

	Min	Max
Q	0.0536	3.4949

Result

Type of curve: single_conc
Comments: In addition to the SAXS profile displayed above, a lipase B unfolding series spanning 0 M to 6 M guanidine hydrochloride is included in the full entry zip archive.

	Experimental	Standard
MW	37.2 kDa	37.2 kDa

	Guinier	Guinier error
Forward scattering, I0	1344.93	8.06
Radius of gyration, Rg	2.41 nm	0.08

	Min	Max
Guinier point	10	244