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SASDP35 – Consensus SANS Profile - Xylanase in H2O buffer

Endo-1,4-beta-xylanase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Endo-1,4-beta-xylanase monomer, 21 kDa Trichoderma longibrachiatum protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 22
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q, Hub J, Hura G, Irving T, Jeffries C, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg D, Ryan T, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss T, Whitten A, Wood K, Zuo X
RgGuinier 1.6 nm
Dmax 4.3 nm

SASDP45 – Consensus SANS Profile - Urate oxidase in H2O buffer

Uricase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Uricase tetramer, 136 kDa Aspergillus flavus protein
Buffer: 100 mM Tris, 150 mM NaCl, pH: 8
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 24
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q, Hub J, Hura G, Irving T, Jeffries C, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg D, Ryan T, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss T, Whitten A, Wood K, Zuo X
RgGuinier 3.2 nm
Dmax 9.1 nm

SASDP55 – Consensus SANS Profile - Xylose isomerase in H2O buffer

Xylose isomerase experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Xylose isomerase tetramer, 173 kDa Streptomyces rubiginosus protein
Buffer: 50 mM Tris, 100 mM NaCl, 1 mM MgCl2, pH: 7.5
Experiment: SANS data collected at (Consensus SAS), Multi-facility, Multiple countries on 2022 Jun 24
A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking Acta Crystallographica Section D Structural Biology 78(11) (2022)
Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland T, Cowieson N, Crossett B, Duff A, Franke D, Gabel F, Gillilan R, Graewert M, Grishaev A, Guss J, Hammel M, Hopkins J, Huang Q, Hub J, Hura G, Irving T, Jeffries C, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg D, Ryan T, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss T, Whitten A, Wood K, Zuo X
RgGuinier 3.3 nm
Dmax 9.7 nm

SASDKS7 – Hydroxypyruvate aldolase (HpcH/HpaI aldolase), wild-type in HEPES, NaCl and MgCl2

HpcH/HpaI aldolase experimental SAS data
GASBOR model
Sample: HpcH/HpaI aldolase hexamer, 165 kDa Rhizorhabdus wittichii RW1 protein
Buffer: 20 mM HEPES, 100 mM NaCl, 20 mg/l MgCl2, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 15
Substrate Induced Movement of the Metal Cofactor between Active and Resting State Angewandte Chemie International Edition (2022)
Marsden S, Wijma H, Mohr M, Justo I, Hagedoorn P, Laustsen J, Jeffries C, Svergun D, Mestrom L, McMillan D, Bento I, Hanefeld U
RgGuinier 3.3 nm
Dmax 9.0 nm
VolumePorod 224 nm3

SASDKT7 – Hydroxypyruvate aldolase (HpcH/HpaI aldolase), S116A mutant in HEPES, NaCl and MgCl2

HpcH/HpaI aldolase (S116A) experimental SAS data
GASBOR model
Sample: HpcH/HpaI aldolase (S116A) hexamer, 165 kDa Sphingomonas wittichii (strain … protein
Buffer: 20 mM HEPES, 100 mM NaCl, 20 mg/l MgCl2, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 15
Substrate Induced Movement of the Metal Cofactor between Active and Resting State Angewandte Chemie International Edition (2022)
Marsden S, Wijma H, Mohr M, Justo I, Hagedoorn P, Laustsen J, Jeffries C, Svergun D, Mestrom L, McMillan D, Bento I, Hanefeld U
RgGuinier 3.3 nm
Dmax 9.1 nm
VolumePorod 222 nm3

SASDKU7 – Hydroxypyruvate aldolase (HpcH/HpaI aldolase), S116C mutant in HEPES, NaCl and MgCl2

HpcH/HpaI aldolase (S116C) experimental SAS data
GASBOR model
Sample: HpcH/HpaI aldolase (S116C) hexamer, 165 kDa Rhizorhabdus wittichii RW1 protein
Buffer: 20 mM HEPES, 100 mM NaCl, 20 mg/l MgCl2, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 15
Substrate Induced Movement of the Metal Cofactor between Active and Resting State Angewandte Chemie International Edition (2022)
Marsden S, Wijma H, Mohr M, Justo I, Hagedoorn P, Laustsen J, Jeffries C, Svergun D, Mestrom L, McMillan D, Bento I, Hanefeld U
RgGuinier 3.3 nm
Dmax 9.0 nm
VolumePorod 223 nm3

SASDNH2 – Complex of Geobacter sulfurreducens pAgo with Sir2-like effector protein

Piwi domain proteinSir2 superfamily protein experimental SAS data
GASBOR model
Sample: Piwi domain protein monomer, 53 kDa Geobacter sulfurreducens (strain … protein
Sir2 superfamily protein monomer, 68 kDa Geobacter sulfurreducens (strain … protein
Buffer: 20 mM TrisHCl, pH 7.5, 5 mM MgCl2, 150 mM NaCl and 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2016 Sep 27
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion Nature Microbiology (2022)
Zaremba M, Dakineviciene D, Golovinas E, Zagorskaitė E, Stankunas E, Lopatina A, Sorek R, Manakova E, Ruksenaite A, Silanskas A, Asmontas S, Grybauskas A, Tylenyte U, Jurgelaitis E, Grigaitis R, Timinskas K, Venclovas Č, Siksnys V
RgGuinier 3.6 nm
Dmax 11.4 nm
VolumePorod 185 nm3

SASDPD3 – Second exon splicing silencer 2p (ESS2p) RNA, apo

The second exon splicing silencer 2p experimental SAS data
AMBER model
Sample: The second exon splicing silencer 2p monomer, 14 kDa RNA
Buffer: 20 mM Bis-Tris, 20 mM NaCl, pH: 6.2
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2017 Nov 1
Encoded Conformational Dynamics of the HIV Splice Site A3 Regulatory Locus: Implications for Differential Binding of hnRNP Splicing Auxiliary Factors. J Mol Biol 434(18):167728 (2022)
Chiu LY, Emery A, Jain N, Sugarman A, Kendrick N, Luo L, Ford W, Swanstrom R, Tolbert BS
RgGuinier 2.1 nm
Dmax 6.9 nm
VolumePorod 21 nm3

SASDPK4 – His-tagged RdfS Excisionase monomeric in solution

DNA-binding protein experimental SAS data
His-tagged RdfS Excisionase monomeric in solution Rg histogram
Sample: DNA-binding protein monomer, 13 kDa Mesorhizobium loti protein
Buffer: 150 mM Tris-HCl, 300 mM NaCl, 5% v/v glycerol, pH: 7.4
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2019 Jun 19
Crystallographic and X-ray scattering study of RdfS, a recombination directionality factor from an integrative and conjugative element Acta Crystallographica Section D Structural Biology 78(10) (2022)
Verdonk C, Marshall A, Ramsay J, Bond C
RgGuinier 2.2 nm
Dmax 9.2 nm
VolumePorod 23 nm3

SASDPH7 – Urate Oxidase SEC-SAXS data (EMBL-P12 bioSAXS beam line at DESY)

Urate Oxidase (Uricase) from Aspergillus flavus experimental SAS data
Urate Oxidase (Uricase) from Aspergillus flavus Kratky plot
Sample: Urate Oxidase (Uricase) from Aspergillus flavus tetramer, 137 kDa Aspergillus flavus protein
Buffer: 100 mM Tris, 150 mM NaCl, 1 % v/v glycerol, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Sep 15
Small-Angle X-ray Scattering data (benchmarking/consensus): EMBL-P12 SAXS beam line, DESY
Clement Blanchet, Melissa Graewert, Cy M Jeffries, Dmitri Svergun
RgGuinier 3.2 nm
Dmax 8.8 nm
VolumePorod 221 nm3