SASDDM3: Carboyxamidomethylated ribonuclease A (unfolded RNAse) - with and...

Basic information

Entry

Database: SASBDB / ID: SASDDM3

Sample

Carboyxamidomethylated ribonuclease A (unfolded RNAse) - with and without urea

• Ribonuclease pancreatic (protein), RNase, Bos taurus

Function / homology

Function:

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

Domain/homology:

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

Component:

Ribonuclease pancreatic

• Biological species: Bos taurus (domestic cattle)
• 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: Carboyxamidomethylated ribonuclease A (unfolded RNAse) - with and without urea; Specimen concentration: 5.97 mg/ml
• Buffer: Name: 10 mM HCl / pH: 1

Entity #17

Name: RNase / Type: protein / Description: Ribonuclease pancreatic / Formula weight: 16.46 / Num. of mol.: 1 / Source: Bos taurus / References: UniProt: P61823
Sequence:

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

Experimental information

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

Scan

Title: Carboyxamidomethylated ribonuclease A (unfolded RNAse) - with and without urea
Measurement date: Jul 29, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.03 sec. / Number of frames: 17 / Unit: 1/nm /

	Min	Max
Q	0.0536	3.4949

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 397 /

	Min	Max
Q	0.3263	3.489
P(R) point	136	532
R	0	9

Result

Type of curve: single_conc
Comments: Included in the additional files of the full-entry zip archive are SAXS data measured from folded RNAse (rnase.dat - also refer to SASBDB entry SASDDL3) as well as unfolded carboyxamidomethylated ribonuclease A (rnaseU.dat) and unfolded RNAse in the presence of 1 M urea (rnaseUU1.dat) or 2 M urea (rnaseUU2.dat).

	Experimental	Standard
MW	13.4 kDa	13.4 kDa

	P(R)	Guinier	Guinier error
Forward scattering, I0	498.2	484.7	5.04
Radius of gyration, Rg	2.55 nm	2.31 nm	0.03

	Min	Max
D	-	9
Guinier point	154	254