Browse by MODEL: Hybrid

SASDEB6 – Staphylococcus aureus glucosamine-6-phosphate deaminase

Glucosamine-6-phosphate deaminase experimental SAS data
PYMOL model
Sample: Glucosamine-6-phosphate deaminase dimer, 57 kDa Staphylococcus aureus protein
Buffer: 20 mM Tris-HCl 150 mM NaCl, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2016 Apr 26
Functional and solution structure studies of amino sugar deacetylase and deaminase enzymes from Staphylococcus aureus. FEBS Lett (2018)
Davies JS, Coombes D, Horne CR, Pearce FG, Friemann R, North RA, Dobson RCJ
RgGuinier 2.7 nm
Dmax 8.9 nm
VolumePorod 84 nm3

SASDEH3 – TubR protein of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR) bound to S48 DNA (Bc-TubR : S48 DNA complex)

S48 DNA strand 1S48 DNA strand 2TubR of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR) experimental SAS data
MOLECULAR DYNAMICS FRAME model
Sample: S48 DNA strand 1 monomer, 21 kDa DNA
S48 DNA strand 2 monomer, 21 kDa DNA
TubR of the pXO1-like plasmid pBc10987 from B. cereus (Bc-TubR) decamer, 137 kDa protein
Buffer: 0.1 M NaCl, 10 mM Tris, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2017 Nov 28
Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid. J Mol Biol (2018)
Hayashi I, Oda T, Sato M, Fuchigami S
RgGuinier 6.1 nm
Dmax 23.0 nm
VolumePorod 305 nm3

SASDD85 – PDZK1 Domain 1-4

Uncharacterized protein C1orf159 experimental SAS data
GASBOR model
Sample: Uncharacterized protein C1orf159 monomer, 53 kDa Homo sapiens protein
Buffer: 20mM Hepes 150 NaCl 0.5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Oct 28
Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution. Structure 26(11):1522-1533.e5 (2018)
Hajizadeh NR, Pieprzyk J, Skopintsev P, Flayhan A, Svergun DI, Löw C
RgGuinier 3.9 nm
Dmax 15.0 nm
VolumePorod 120 nm3

SASDDH3 – Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2)

Transcriptional regulator Lrs14-like protein experimental SAS data
DAMMIF model
Sample: Transcriptional regulator Lrs14-like protein dimer, 33 kDa Sulfolobus acidocaldarius protein
Buffer: 300 mM NaCl, 20 mM HEPES, pH 7.5, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2016 May 5
Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius. Acta Crystallogr D Struct Biol 74(Pt 11):1105-1114 (2018)
Vogt MS, Völpel SL, Albers SV, Essen LO, Banerjee A
RgGuinier 2.9 nm
Dmax 10.0 nm
VolumePorod 57 nm3

SASDD45 – Type II toxin-antitoxin system HicB family antitoxin - HicB protein

Type II toxin-antitoxin system HicB family antitoxin experimental SAS data
PYMOL model
Sample: Type II toxin-antitoxin system HicB family antitoxin tetramer, 63 kDa Burkholderia pseudomallei protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2016 Jul 28
The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA. J Biol Chem (2018)
Winter AJ, Williams C, Isupov MN, Crocker H, Gromova M, Marsh P, Wilkinson OJ, Dillingham MS, Harmer NJ, Titball RW, Crump MP
RgGuinier 3.0 nm
Dmax 10.5 nm
VolumePorod 112 nm3

SASDD55 – Type II toxin-antitoxin system HicB family antitoxin - HicB protein - bound to addiction module toxin, HicA

Type II toxin-antitoxin system HicB family antitoxinAddiction module toxin, HicA experimental SAS data
PYMOL model
Sample: Type II toxin-antitoxin system HicB family antitoxin tetramer, 63 kDa Burkholderia pseudomallei protein
Addiction module toxin, HicA monomer, 7 kDa Burkholderia pseudomallei protein
Buffer: 25 mM Tris, 150 mM NaCl, pH: 7.5
Experiment: SAXS data collected at B21, Diamond Light Source on 2016 Jul 27
The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA. J Biol Chem (2018)
Winter AJ, Williams C, Isupov MN, Crocker H, Gromova M, Marsh P, Wilkinson OJ, Dillingham MS, Harmer NJ, Titball RW, Crump MP
RgGuinier 3.2 nm
Dmax 11.0 nm
VolumePorod 110 nm3

SASDJW2 – Modification dependent EcoKMcrA restriction endonuclease

5-methylcytosine-specific restriction enzyme A experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: 5-methylcytosine-specific restriction enzyme A dimer, 65 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 3.7 nm
Dmax 13.0 nm
VolumePorod 95 nm3

SASDJX2 – Modification dependent EcoKMcrA restriction endonuclease in complex with cognate hemimethylated 12bp oligoduplex

cognate hemimethylated 12-bp oligoduplex5-methylcytosine-specific restriction enzyme A experimental SAS data
SASREF model
Sample: Cognate hemimethylated 12-bp oligoduplex dimer, 15 kDa DNA
5-methylcytosine-specific restriction enzyme A dimer, 65 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 3.9 nm
Dmax 13.5 nm
VolumePorod 69 nm3

SASDJY2 – N-terminal domain of modification dependent EcoKMcrA restriction endonuclease

5-methylcytosine-specific restriction enzyme A (N-terminal domain) experimental SAS data
OTHER model
Sample: 5-methylcytosine-specific restriction enzyme A (N-terminal domain) monomer, 21 kDa Escherichia coli protein
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide, 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 2.1 nm
Dmax 7.5 nm
VolumePorod 29 nm3

SASDJZ2 – N-terminal domain of modification dependent EcoKMcrA restriction endonuclease in complex with cognate hemimethylated 12bp oligoduplex

5-methylcytosine-specific restriction enzyme A (N-terminal domain)cognate hemimethylated 12-bp oligoduplex experimental SAS data
OTHER model
Sample: 5-methylcytosine-specific restriction enzyme A (N-terminal domain) monomer, 21 kDa Escherichia coli protein
Cognate hemimethylated 12-bp oligoduplex monomer, 7 kDa DNA
Buffer: 20 mM Tris–HCl pH 7.5, 200 mM KCl, 0.1 mM EDTA, 0.01% (w/v) sodium azide and 1 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 May 24
Activity and structure of EcoKMcrA. Nucleic Acids Res 46(18):9829-9841 (2018)
Czapinska H, Kowalska M, Zagorskaite E, Manakova E, Slyvka A, Xu SY, Siksnys V, Sasnauskas G, Bochtler M
RgGuinier 2.1 nm
Dmax 7.5 nm
VolumePorod 29 nm3