Browse by MODEL: Ab initio only

SASDPX2 – TIP60 (K67E) mutant (dimer) with EDTA

TIP60 (K67E) mutant with EDTA experimental SAS data
DAMMIN model
Sample: TIP60 (K67E) mutant with EDTA dimer, 36 kDa Artificial protein protein
Buffer: 25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol, pH: 8
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2021 May 23
Reversible Assembly of an Artificial Protein Nanocage Using Alkaline Earth Metal Ions. J Am Chem Soc (2022)
Ohara N, Kawakami N, Arai R, Adachi N, Moriya T, Kawasaki M, Miyamoto K
RgGuinier 3.7 nm
Dmax 12.0 nm

SASDPY2 – SARS-CoV-2 non-structural protein 7-8 (nsp7-8) polyprotein monomer

Replicase polyprotein 1ab experimental SAS data
DAMMIF model
Sample: Replicase polyprotein 1ab monomer, 31 kDa Severe acute respiratory … protein
Buffer: 50 mM Tris, 500 mM NaCl, 5% glycerol, and 1 mM TCEP, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Oct 15
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 2.5 nm
Dmax 8.8 nm
VolumePorod 50 nm3

SASDP23 – SARS-CoV-2 non-structural protein 7-11 (nsp7-11) polyprotein monomer

Replicase polyprotein 1a experimental SAS data
DAMMIF model
Sample: Replicase polyprotein 1a monomer, 60 kDa Severe acute respiratory … protein
Buffer: 20 mM HEPES, 10% glycerol, 500 mM NaCl, 5 mM DTT, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Nov 14
Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 8(49):eadd2191 (2022)
Yadav R, Courouble VV, Dey SK, Harrison JJEK, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E
RgGuinier 3.5 nm
Dmax 15.6 nm
VolumePorod 102 nm3

SASDMG9 – Multidrug resistance operon repressor (MexR) of the MexAB-OprM multidrug efflux pump operon of Pseudomonas aeruginosa

Multidrug resistance operon repressor experimental SAS data
DAMFILT model
Sample: Multidrug resistance operon repressor dimer, 32 kDa Pseudomonas aeruginosa protein
Buffer: 20mM HEPES, 150mM NaCl, 10mM DTT, 1% v/v glycerol, pH: 7.1
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Nov 23
Small-angle X-ray and neutron scattering of MexR and its complex with DNA supports a conformational selection binding model Biophysical Journal (2022)
Caporaletti F, Pietras Z, Morad V, Mårtensson L, Gabel F, Wallner B, Martel A, Sunnerhagen M
RgGuinier 2.3 nm
Dmax 7.7 nm
VolumePorod 56 nm3

SASDQ48 – Minimal proline dehydrogenase domain of proline utilization A (SmPutADeltaAlpha2) 1.1 mg/mL

Minimal proline dehydrogenase domain of proline utilization A (design #2) experimental SAS data
OTHER model
Sample: Minimal proline dehydrogenase domain of proline utilization A (design #2) dimer, 87 kDa Sinorhizobium meliloti protein
Buffer: 25 mM HEPES pH 7.6, 150 mM NaCl, and 1mM TCEP, pH: 7.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2022 Apr 12
Structure-based engineering of minimal Proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel (2022)
Bogner AN, Ji J, Tanner JJ
RgGuinier 2.7 nm
Dmax 9.5 nm
VolumePorod 102 nm3

SASDQ58 – Minimal proline dehydrogenase domain of proline utilization A (SmPutADeltaAlpha2) 2.3 mg/mL

Minimal proline dehydrogenase domain of proline utilization A (design #2) experimental SAS data
OTHER model
Sample: Minimal proline dehydrogenase domain of proline utilization A (design #2) dimer, 87 kDa Sinorhizobium meliloti protein
Buffer: 25 mM HEPES pH 7.6, 150 mM NaCl, and 1mM TCEP, pH: 7.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2022 Apr 12
Structure-based engineering of minimal Proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel (2022)
Bogner AN, Ji J, Tanner JJ
RgGuinier 2.9 nm
Dmax 9.7 nm
VolumePorod 102 nm3

SASDQ68 – Minimal proline dehydrogenase domain of proline utilization A (SmPutADeltaAlpha2) 3.4 mg/mL

Minimal proline dehydrogenase domain of proline utilization A (design #2) experimental SAS data
OTHER model
Sample: Minimal proline dehydrogenase domain of proline utilization A (design #2) dimer, 87 kDa Sinorhizobium meliloti protein
Buffer: 25 mM HEPES pH 7.6, 150 mM NaCl, and 1mM TCEP, pH: 7.6
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2022 Apr 12
Structure-based engineering of minimal Proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel (2022)
Bogner AN, Ji J, Tanner JJ
RgGuinier 3.0 nm
Dmax 9.8 nm
VolumePorod 108 nm3

SASDPM4 – Apo SH2-SH3-SH2 domains from p120RasGAP

Ras GTPase-activating protein 1 experimental SAS data
DAMMIF model
Sample: Ras GTPase-activating protein 1 monomer, 101 kDa Homo sapiens protein
Buffer: 20 mM Tris pH 8 350 mM NaCl 1 mM DTT, pH: 8
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Dec 12
Tandem engagement of phosphotyrosines by the dual SH2 domains of p120RasGAP. Structure (2022)
Stiegler AL, Vish KJ, Boggon TJ
RgGuinier 2.6 nm
Dmax 10.3 nm
VolumePorod 41 nm3

SASDFE6 – Sliding beta clamp

Beta sliding clamp experimental SAS data
GASBOR model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris pH 8.0, 200 mM NaCl , 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 15
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R
RgGuinier 3.7 nm
Dmax 10.3 nm
VolumePorod 186 nm3

SASDFF6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp complex

Beta sliding clampProbable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) experimental SAS data
DAMMIF model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) monomer, 33 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 15
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R
RgGuinier 3.5 nm
Dmax 11.3 nm
VolumePorod 98 nm3