Browse by MODEL: Ab initio only

SASDGX3 – 3'SL from Zika virus

3'SL from Zika virus experimental SAS data
DAMFILT model
Sample: 3'SL from Zika virus monomer, 32 kDa Zika virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at 12-ID-B SAXS/WAXS, Advanced Photon Source (APS), Argonne National Laboratory on 2016 Dec 9
Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution. EMBO Rep 20(11):e47016 (2019)
Zhang Y, Zhang Y, Liu ZY, Cheng ML, Ma J, Wang Y, Qin CF, Fang X
RgGuinier 3.9 nm
Dmax 14.1 nm
VolumePorod 52 nm3

SASDGY3 – 3'SL from West Nile virus

3'SL from West Nile virus experimental SAS data
DAMMIF model
Sample: 3'SL from West Nile virus monomer, 31 kDa West Nile virus RNA
Buffer: 20mM Tris-HCl, 100mM NaCl, 5mM MgCl2, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2017 Apr 7
Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution. EMBO Rep 20(11):e47016 (2019)
Zhang Y, Zhang Y, Liu ZY, Cheng ML, Ma J, Wang Y, Qin CF, Fang X
RgGuinier 3.5 nm
Dmax 13.2 nm
VolumePorod 39 nm3

SASDFD7 – Pseudomonas putida CBB5 NdmAB complex - static

Methylxanthine N1-demethylase NdmAMethylxanthine N3-demethylase NdmB experimental SAS data
DAMMIF model
Sample: Methylxanthine N1-demethylase NdmA trimer, 127 kDa Pseudomonas putida protein
Methylxanthine N3-demethylase NdmB trimer, 129 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP 10% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at 4C, Pohang Accelerator Laboratory on 2018 Jul 27
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 4.5 nm
Dmax 12.3 nm

SASDFE7 – Pseudomonas putida CBB5 mCherry-NdmA/NdmB complex - static

Methylxanthine N1-demethylase NdmAMethylxanthine N3-demethylase NdmB experimental SAS data
DAMMIF model
Sample: Methylxanthine N1-demethylase NdmA trimer, 207 kDa Pseudomonas putida protein
Methylxanthine N3-demethylase NdmB trimer, 129 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP 10% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at 4C, Pohang Accelerator Laboratory on 2018 Jul 27
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 5.4 nm
Dmax 13.8 nm

SASDFF7 – Pseudomonas putida CBB5 NdmA hexamer

Methylxanthine N1-demethylase NdmA experimental SAS data
DAMMIF model
Sample: Methylxanthine N1-demethylase NdmA hexamer, 254 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 May 21
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 4.2 nm
Dmax 11.0 nm

SASDFG7 – Pseudomonas putida CBB5 NdmB hexamer

Methylxanthine N3-demethylase NdmB experimental SAS data
DAMMIF model
Sample: Methylxanthine N3-demethylase NdmB hexamer, 258 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 May 21
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 4.3 nm
Dmax 12.2 nm

SASDFH7 – Pseudomonas putida CBB5 NdmAB complex

Methylxanthine N1-demethylase NdmAMethylxanthine N3-demethylase NdmB experimental SAS data
DAMMIF model
Sample: Methylxanthine N1-demethylase NdmA trimer, 127 kDa Pseudomonas putida protein
Methylxanthine N3-demethylase NdmB trimer, 129 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP, pH: 7.5
Experiment: SAXS data collected at BL-10C, Photon Factory (PF), High Energy Accelerator Research Organization (KEK) on 2018 May 21
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 4.2 nm
Dmax 10.9 nm

SASDFJ7 – Pseudomonas putida CBB5 mCherry-NdmA/ECFP-NdmB complex - static

Methylxanthine N1-demethylase NdmAMethylxanthine N3-demethylase NdmB experimental SAS data
DAMMIF model
Sample: Methylxanthine N1-demethylase NdmA trimer, 207 kDa Pseudomonas putida protein
Methylxanthine N3-demethylase NdmB trimer, 208 kDa Pseudomonas putida protein
Buffer: 20 mM HEPES 150 mM NaCl 2 mM TCEP 10% v/v glycerol, pH: 7.5
Experiment: SAXS data collected at 4C, Pohang Accelerator Laboratory on 2018 Jul 27
Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J Mol Biol 431(19):3647-3661 (2019)
Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK
RgGuinier 5.6 nm
Dmax 19.1 nm

SASDDA6 – Class I chitinase 2 from Agave tequilana

Chitinase 2 experimental SAS data
DAMMIF model
Sample: Chitinase 2 monomer, 32 kDa Agave tequilana protein
Buffer: MES 50 mM, pH: 6
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2017 Apr 19
A biophysical and structural study of two chitinases from Agave tequilana and their potential role as defense proteins. FEBS J (2019)
Sierra-Gómez Y, Rodríguez-Hernández A, Cano-Sánchez P, Gómez-Velasco H, Hernández-Santoyo A, Siliqi D, Rodríguez-Romero A
RgGuinier 2.4 nm
Dmax 9.8 nm
VolumePorod 49 nm3

SASDDE7 – Class I chitinase 1 from Agave tequilana

Chitinase 1 experimental SAS data
DAMMIF model
Sample: Chitinase 1 monomer, 32 kDa Agave tequilana protein
Buffer: MES 50 mM, pH: 6
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2017 Apr 26
A biophysical and structural study of two chitinases from Agave tequilana and their potential role as defense proteins. FEBS J (2019)
Sierra-Gómez Y, Rodríguez-Hernández A, Cano-Sánchez P, Gómez-Velasco H, Hernández-Santoyo A, Siliqi D, Rodríguez-Romero A
RgGuinier 2.6 nm
Dmax 9.7 nm
VolumePorod 52 nm3