SASDA69: slp-B53 with Mg2+ (S-layer protein, Slp1)

Basic information

• Entry: Database: SASBDB / ID: SASDA69

Sample

slp-B53 with Mg2+

• S-layer protein (protein), Slp1, Lysinibacillus sphaericus

• Function / homology: S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Invasin/intimin cell-adhesion fragments / Immunoglobulin-like fold / Slp1
• Biological species: Lysinibacillus sphaericus (bacteria)
• Citation: Journal: Eur Biophys J / Year: 2017; Title: Analysis of self-assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus.; Authors: Jun Liu / Sven Falke / Bjoern Drobot / Dominik Oberthuer / Alexey Kikhney / Tobias Guenther / Karim Fahmy / Dmitri Svergun / Christian Betzel / Johannes Raff / ; Abstract: The formation of stable and functional surface layers (S-layers) via self-assembly of surface-layer proteins on the cell surface is a dynamic and complex process. S-layers facilitate a number of important biological functions, e.g., providing protection and mediating selective exchange of molecules and thereby functioning as molecular sieves. Furthermore, S-layers selectively bind several metal ions including uranium, palladium, gold, and europium, some of them with high affinity. Most current research on surface layers focuses on investigating crystalline arrays of protein subunits in Archaea and bacteria. In this work, several complementary analytical techniques and methods have been applied to examine structure-function relationships and dynamics for assembly of S-layer protein slp-B53 from Lysinibacillus sphaericus: (1) The secondary structure of the S-layer protein was analyzed by circular dichroism spectroscopy; (2) Small-angle X-ray scattering was applied to gain insights into the three-dimensional structure in solution; (3) The interaction with bivalent cations was followed by differential scanning calorimetry; (4) The dynamics and time-dependent assembly of S-layers were followed by applying dynamic light scattering; (5) The two-dimensional structure of the paracrystalline S-layer lattice was examined by atomic force microscopy. The data obtained provide essential structural insights into the mechanism of S-layer self-assembly, particularly with respect to binding of bivalent cations, i.e., Mg and Ca. Furthermore, the results obtained highlight potential applications of S-layers in the fields of micromaterials and nanobiotechnology by providing engineered or individual symmetric thin protein layers, e.g., for protective, antimicrobial, or otherwise functionalized surfaces.

Contact author

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

Models

• Model #412: ; Type: dummy / Software: (r5577) / Radius of dummy atoms: 5.80 A / Chi-square value: 1.858; Search similar-shape structures of this assembly by Omokage search (details)
• Model #543: ; Type: atomic / Software: (2.7.1) / Symmetry: P1 / Comment: ~40% by volume / Chi-square value: 2.42; Search similar-shape structures of this assembly by Omokage search (details)
• Model #544: ; Type: atomic / Software: (2.7.1) / Symmetry: P2 / Comment: ~60% by volume / Chi-square value: 2.42; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: slp-B53 with Mg2+ / Specimen concentration: 1.00-7.50
• Buffer: Name: Water with Mg2+ / Composition: Mg2+

Entity #271

Name: Slp1 / Type: protein / Description: S-layer protein / Formula weight: 116.01 / Num. of mol.: 1 / Source: Lysinibacillus sphaericus / References: UniProt: M4N8T6
Sequence:

manqpkkykk fvataatatl vasaivpvas aagfsdvagn dhevainalv eagiingyad gtfkpnqsin rgqvvkllgr wleaqgqeip adwetkqrft dlpvtaeael vkyaalakda gvfagsngnl nhtqtmqrqq mavvlvraik eissvdlvad ykkagfvtei tdleaaysae qrnaivaley agitnvskfn passitrgqf asflhrtinn vmepeagvst vkainnttve vtfdtevdnv qalnflisdl evknaavkqt nkkvvvltta aqtadkeytv slgedkigtf kgiaavnptk vemvssatqg klgqqvtvka qvtvaegqsk agipvtfyvp gkndavypti tgeaftdeng vasysytrya agtdavtaya tgdrskfatg hvfwgvdtil aieevttgat innganktyk ivyknattgk peanktfnvs flenidvtsn klanatvngv avsqlsnasv vkaaqittds kgeatftvsg tnaevtpvvf eaeaivtsgs ttvtgysqky sasslqttaa kvkfgalqae ytidvtregg evaargvnng reykvtvkdk dgklakneii nvafnedldr vistetkayf idvdkddkqt isstpskisv ktndkgeatf vigsdkendy atpvawidin ssnakdgqld egepktiaqi shfqdayldg gavkaylapk fdksvtefkg netatfkasl vnqsgkdmpn tsiknvtyti fntgsndvqv ngqvispnrs ytvssetlks tdltvtsvng kttsvkviat gvakntdgkd yaftskeata kftsltdvgt qitadvvevn dkelvfagkd pislkdakfy niygaelvgv dafkddlvnn atyatgvvvt ftedkdgkka frvaragteg kvnvgalklt naditvassp attttaatas itltvgetlv innqsytyna gagtadanhy nslvdlagki sadsktggvk avvnagstgl dltgnakgen ftykigalta vstingvvgk davdqqitft fsaavnvkan dsvlingtva gtvasvsgsk vvvkiaqasa iptttaitaf tvngtvlksk ltnsdvtigs itlk

Experimental information

• Beam: Instrument name: PETRA III 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: slp-B53 with Mg / Measurement date: Jun 2, 2015 / Storage temperature: 20 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.027	4.8012

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 411 /

	Min	Max
Q	0.0903604	1.17362
P(R) point	1	411
R	0	29

Result

Type of curve: extrapolated / Comments: slp-B53 with Mg /

	Experimental	Porod
MW	178 kDa	373 kDa
Volume	-	596.6 nm3

	Guinier	P(R)	Guinier error
Forward scattering, I0	8079.61	-	-
Radius of gyration, Rg	6.55 nm	7.275 nm	0.62

	Min	Max
D	-	29
Guinier point	25	66