SASDBK3: Bovine serum albumin, dimer from SEC-SAXS (Bovine serum albumin, ...

Basic information

• Entry: Database: SASBDB / ID: SASDBK3

Sample

Bovine serum albumin, dimer from SEC-SAXS

• Bovine serum albumin, dimer (protein), BSA dimer, 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: Nat Protoc / Year: 2016; Title: Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments.; Authors: Cy M Jeffries / Melissa A Graewert / Clément E Blanchet / David B Langley / Andrew E Whitten / Dmitri I Svergun / ; Abstract: Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions from all atoms within the illuminated sample volume, including the solvent and buffer components, as well as the macromolecules of interest. To obtain structural information, it is essential to prepare an exactly matched solvent blank so that background scattering contributions can be accurately subtracted from the sample scattering to obtain the net scattering from the macromolecules in the sample. In addition, sample heterogeneity caused by contaminants, aggregates, mismatched solvents, radiation damage or other factors can severely influence and complicate data analysis, so it is essential that the samples be pure and monodisperse for the duration of the experiment. This protocol outlines the basic physics of SAXS and SANS, and it reveals how the underlying conceptual principles of the techniques ultimately 'translate' into practical laboratory guidance for the production of samples of sufficiently high quality for scattering experiments. The procedure describes how to prepare and characterize protein and nucleic acid samples for both SAXS and SANS using gel electrophoresis, size-exclusion chromatography (SEC) and light scattering. Also included are procedures that are specific to X-rays (in-line SEC-SAXS) and neutrons, specifically preparing samples for contrast matching or variation experiments and deuterium labeling of proteins.

Contact author

• Dmitri Svergun
• Melissa Graewert
• Clement Blanchet
• Cy M Jeffries

Models

• Model #448: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.044; Search similar-shape structures of this assembly by Omokage search (details)
• Model #450: ; Type: dummy / Radius of dummy atoms: 3.60 A / Chi-square value: 1.104601 / P-value: 0.339000; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Bovine serum albumin, dimer from SEC-SAXS
• Buffer: Name: 25 mM Tris 150 mM NaCl 3% (v/v) glycerol / Concentration: 25.00 mM / pH: 7.5 / Composition: 150 mM NaCl 3% v/v glycerol

Entity #299

Name: BSA dimer / Type: protein / Description: Bovine serum albumin, dimer / Formula weight: 66.462 / Num. of mol.: 2 / 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: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Bovine serum albumin, dimer / Measurement date: Jan 23, 2014 / Storage temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 3600 / Unit: 1/nm /

	Min	Max
Q	0.0779	3.4555

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 427 /

	Min	Max
Q	0.07526	3.441
P(R) point	21	447
R	0	12.71

Result

Type of curve: other /

	Experimental	Porod
MW	133.6 kDa	125.9 kDa
Volume	-	201.5 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	219.7	1.26	217.8	1.32
Radius of gyration, Rg	4.02 nm	0.03	3.89 nm	0.06

	Min	Max
D	-	12.7
Guinier point	1	98