Browse by MODEL: Ab initio only

SASDEX6 – Cold-active AMS8 lipase in the presence of calcium (without polyhistidine affinity tag)

LipAMS8 experimental SAS data
DAMMIF model
Sample: LipAMS8 monomer, 50 kDa Pseudomonas sp. AMS8 protein
Buffer: 50 mM Tris HCl, 5 mM CaCl2, pH: 8
Experiment: SAXS data collected at BL1.3W, Synchrotron Light Research Institute (SLRI) on 2018 Mar 6
Structural interpretations of a flexible cold-active AMS8 lipase by combining small-angle X-ray scattering and molecular dynamics simulation (SAXS-MD). Int J Biol Macromol (2022)
Yaacob N, Kamonsutthipaijit N, Soontaranon S, Leow TC, Rahman RNZRA, Ali MSM
RgGuinier 2.9 nm
Dmax 9.8 nm
VolumePorod 87 nm3

SASDN97 – Human thryoglobulin measured using SEC-SAXS

Thyroglobulin experimental SAS data
DAMMIN model
Sample: Thyroglobulin dimer, 610 kDa Homo sapiens protein
Buffer: phosphate buffered saline, 150mM NaCl, pH: 8
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2020 Jul 17
Thyroglobulin - human and bovine SAXS/WAXS data
James Byrnes
RgGuinier 7.7 nm
Dmax 26.3 nm
VolumePorod 1800 nm3

SASDNA7 – Bovine thyroglobulin in phosphate buffered saline/NaCl

Thyroglobulin experimental SAS data
DAMMIF model
Sample: Thyroglobulin dimer, 606 kDa Bos taurus protein
Buffer: phosphate buffered saline, 150mM NaCl, pH: 8
Experiment: SAXS data collected at 16-ID (LiX), National Synchrotron Light Source II (NSLS-II) on 2020 Jul 17
Thyroglobulin - human and bovine SAXS/WAXS data
James Byrnes
RgGuinier 8.1 nm
Dmax 29.8 nm
VolumePorod 1950 nm3

SASDJJ5 – Histone H2A:H2B:H3:H4 complex with aprataxin and polynucleotide kinase like factor (APLF) acidic domain

Aprataxin and PNK-like factor (acidic domain)Histone H2AHistone H2BHistone H3Histone H4 experimental SAS data
DAMMIF model
Sample: Aprataxin and PNK-like factor (acidic domain) dimer, 15 kDa Homo sapiens protein
Histone H2A dimer, 26 kDa Drosophila melanogaster protein
Histone H2B dimer, 27 kDa Drosophila melanogaster protein
Histone H3 dimer, 30 kDa Drosophila melanogaster protein
Histone H4 dimer, 23 kDa Drosophila melanogaster protein
Buffer: 25 mM NaPi, 300 mM NaCl, 3% v/v glycerol, 1 mM DTT,, pH: 7
Experiment: SAXS data collected at EMBL P12, PETRA III on 2018 Jul 10
Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Sci Adv 8(30):eabo0517 (2022)
Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H
RgGuinier 3.7 nm
Dmax 10.8 nm
VolumePorod 260 nm3

SASDFG5 – His-RuvBl1/RuvBl2 dodecamer

RuvB-like 1RuvB-like 2 experimental SAS data
DAMMIF model
Sample: RuvB-like 1 hexamer, 311 kDa Homo sapiens protein
RuvB-like 2 hexamer, 311 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 150 mM NaCl, 1% glycerol, 5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Mar 21
Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. J Mol Biol :167760 (2022)
Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X
RgGuinier 6.2 nm
Dmax 20.0 nm
VolumePorod 1490 nm3

SASDFH5 – DPCD His-RuvBl1/RuvBl2 hexamer complex

Protein DPCDRuvB-like 1RuvB-like 2 experimental SAS data
GASBOR model
Sample: Protein DPCD trimer, 71 kDa Homo sapiens protein
RuvB-like 1 trimer, 155 kDa Homo sapiens protein
RuvB-like 2 trimer, 156 kDa Homo sapiens protein
Buffer: 20 mM HEPES, 150 mM NaCl, 1% glycerol, 5 mM TCEP, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2019 Mar 21
Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. J Mol Biol :167760 (2022)
Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X
RgGuinier 5.4 nm
Dmax 15.9 nm
VolumePorod 856 nm3

SASDNU5 – Lysin from Streptococcus phage P7951 ∆1-208

lysin [Streptococcus phage P7951] experimental SAS data
DAMFILT model
Sample: Lysin [Streptococcus phage P7951] hexamer, 65 kDa Streptococcus phage P7951 protein
Buffer: 50 mM HEPES, 500 mM NaCl, and 1% glycerol, pH: 7
Experiment: SAXS data collected at BM29, ESRF on 2021 Nov 21
On the Occurrence and Multimerization of Two-Polypeptide Phage Endolysins Encoded in Single Genes. Microbiol Spectr :e0103722 (2022)
Pinto D, Gonçalo R, Louro M, Silva MS, Hernandez G, Cordeiro TN, Cordeiro C, São-José C
RgGuinier 3.1 nm
Dmax 10.1 nm
VolumePorod 111 nm3

SASDNE5 – Acinetobacter baumannii aconitate hydratase B, monomer/dimer mixed fraction

Aconitate hydratase B experimental SAS data
GASBOR model
Sample: Aconitate hydratase B, 96 kDa Acinetobacter baumannii protein
Buffer: 100 mM NaCl, 20 mM Tris, 1 mM DTT, 3% v/v glycerol, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Dec 3
Recombinant AcnB, NrdR and RibD of Acinetobacter baumannii and their potential interaction with DNA adenine methyltransferase AamA. Protein Expr Purif :106134 (2022)
Weber K, Doellinger J, Jeffries CM, Wilharm G
RgGuinier 4.0 nm
Dmax 14.0 nm
VolumePorod 230 nm3

SASDPJ4 – N-terminal domain of EccA5

ESX-5 secretion system protein EccA5 experimental SAS data
DAMMIF model
Sample: ESX-5 secretion system protein EccA5 monomer, 31 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 20 mM Tris, 150 mM NaCl, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2018 Mar 9
Structural and Biophysical characterization of N-terminal domain of EccA5 from Mycobacterium tuberculosis.
Jyoti Vishwakarma
RgGuinier 2.6 nm
Dmax 7.8 nm
VolumePorod 57 nm3

SASDNK9 – Monomer of the full-length apo-polyketide synthase Pks13 of Mycobacterium tuberculosis

Polyketide synthase Pks13 experimental SAS data
DAMMIN model
Sample: Polyketide synthase Pks13 monomer, 188 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 50 mM Tris-HCl, 50 mM NaCl, pH: 8
Experiment: SAXS data collected at SWING, SOLEIL on 2013 Mar 1
Solution structure of the type I polyketide synthase Pks13 from Mycobacterium tuberculosis. BMC Biol 20(1):147 (2022)
Bon C, Cabantous S, Julien S, Guillet V, Chalut C, Rima J, Brison Y, Malaga W, Sanchez-Dafun A, Gavalda S, Quémard A, Marcoux J, Waldo GS, Guilhot C, Mourey L
RgGuinier 7.3 nm
Dmax 24.8 nm
VolumePorod 480 nm3