SASDDN3: Bovine serum albumin mixture: averaged and individual data frames...

Basic information

Entry

Database: SASBDB / ID: SASDDN3

Sample

Bovine serum albumin mixture: averaged and individual data frames (subtracted and unsubtracted test sets)

• Bovine serum albumin (protein), BSA, Bos taurus

Function / homology

Function:

enterobactin binding / cellular response to calcium ion starvation / negative regulation of mitochondrial depolarization / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / protein-containing complex / DNA binding / extracellular space / extracellular region / metal ion binding / cytoplasm

Domain/homology:

Serum albumin/Alpha-fetoprotein/Afamin / ALB/AFP/VDB / Serum albumin, N-terminal / Serum albumin, conserved site / Serum albumin-like / Serum albumin family / Albumin domain signature. / Albumin domain profile. / serum albumin

Component:

Albumin

• Biological species: Bos taurus (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: Bovine serum albumin mixture: averaged and individual data frames (subtracted and unsubtracted test sets); Specimen concentration: 2.25 mg/ml
• Buffer: Name: 50 mM HEPES / Concentration: 50.00 mM / pH: 7.5

Entity #969

Name: BSA / Type: protein / Description: Bovine serum albumin / Formula weight: 66.462 / Source: Bos taurus / References: UniProt: P02769
Sequence:

DTHKSEIAHR FKDLGEEHFK GLVLIAFSQY LQQCPFDEHV KLVNELTEFA KTCVADESHA GCEKSLHTLF GDELCKVASL RETYGDMADC CEKQEPERNE CFLSHKDDSP DLPKLKPDPN TLCDEFKADE KKFWGKYLYE IARRHPYFYA PELLYYANKY NGVFQECCQA EDKGACLLPK IETMREKVLT SSARQRLRCA SIQKFGERAL KAWSVARLSQ KFPKAEFVEV TKLVTDLTKV HKECCHGDLL ECADDRADLA KYICDNQDTI SSKLKECCDK PLLEKSHCIA EVEKDAIPEN LPPLTADFAE DKDVCKNYQE AKDAFLGSFL YEYSRRHPEY AVSVLLRLAK EYEATLEECC AKDDPHACYS TVFDKLKHLV DEPQNLIKQN CDQFEKLGEY GFQNALIVRY TRKVPQVSTP TLVEVSRSLG KVGTRCCTKP ESERMPCTED YLSLILNRLC VLHEKTPVSE KVTKCCTESL VNRRPCFSAL TPDETYVPKA FDEKLFTFHA DICTLPDTEK QIKKQTALVE LLKHKPKATE EQLKTVMENF VAFVDKCCAA DDKEACFAVE GPKLVVSTQT ALA

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: Bovine serum albumin (mixture) in HEPES / Measurement date: Sep 25, 2016 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 100 / Unit: 1/nm /

	Min	Max
Q	0.0134	3.7904

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1385 /

	Min	Max
Q	0.0447329	2.9376
P(R) point	1	1385
R	0	11

Result

Type of curve: single_conc
Comments: The data displayed in this entry represents the averaged 1D-SAXS profile obtained from 100 individual SAXS data frames. Included in the full entry zip-archive are each of the individual subtracted SAXS profiles as well as each individual sample and buffer frame (100 in total).

	Experimental	Porod
MW	72.4 kDa	73 kDa
Volume	-	116.7 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	11640	11597.7	7.33
Radius of gyration, Rg	3.067 nm	3.02 nm	0.18

	Min	Max
D	-	11
Guinier point	21	200