Browse by MODEL: Hybrid

SASDKX9 – Transcription factors MAX and NF-Y bound to a CCAAT DNA box(48bp)

Protein max (Isoform 2, short, 13-21: missing)Nuclear transcription factor Y subunit alphaNuclear transcription factor Y subunit betaNuclear transcription factor Y subunit gammaDNA 48bp experimental SAS data
DAMMIN model
Sample: Protein max (Isoform 2, short, 13-21: missing) dimer, 39 kDa Homo sapiens protein
Nuclear transcription factor Y subunit alpha monomer, 10 kDa Homo sapiens protein
Nuclear transcription factor Y subunit beta monomer, 11 kDa Homo sapiens protein
Nuclear transcription factor Y subunit gamma monomer, 11 kDa Homo sapiens protein
DNA 48bp monomer, 30 kDa DNA
Buffer: 100 mM cacodylate buffer, pH: 6.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2012 Dec 10
The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding International Journal of Biological Macromolecules (2021)
Bernardini A, Lorenzo M, Chaves-Sanjuan A, Swuec P, Pigni M, Saad D, Konarev P, Graewert M, Valentini E, Svergun D, Nardini M, Mantovani R, Gnesutta N
RgGuinier 5.2 nm
Dmax 17.0 nm
VolumePorod 151 nm3

SASDL29 – SAXS data from RW4-MPC at 1 mg/ml at 283 K

Metapyrocatechase experimental SAS data
MODELLER model
Sample: Metapyrocatechase tetramer, 139 kDa Novosphingobium sp. AAP93 protein
Buffer: 20 mM Tris-HCl 250 mM NaCl, pH 8.0, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR - Institute of Microbial Technology (IMTech) on 2019 Dec 20
Shape-function of a novel metapyrocatechase, RW4-MPC: Metagenomics to SAXS data based insight into deciphering regulators of function. Int J Biol Macromol 188:1012-1024 (2021)
Vasudeva G, Sidhu C, Kalidas N, Ashish, Pinnaka AK
RgGuinier 3.7 nm
Dmax 10.2 nm

SASDF59 – LIM domain-binding protein 1 (Ldb1) self association domain

LIM domain-binding protein 1 experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: LIM domain-binding protein 1 dimer, 45 kDa Mus musculus protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP,, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 19
Self association of LIM domain binding protein 1, LDB1
Jacqueline Matthews
RgGuinier 2.5 nm
Dmax 8.8 nm
VolumePorod 80 nm3

SASDF69 – LIM domain-binding protein 1 (Ldb1) self association domain L87E

LIM domain-binding protein 1, L87E experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: LIM domain-binding protein 1, L87E dimer, 45 kDa Mus musculus protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP,, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 19
Self association of LIM domain binding protein 1, LDB1
Jacqueline Matthews
RgGuinier 2.4 nm
Dmax 7.8 nm
VolumePorod 84 nm3

SASDF79 – LIM domain-binding protein 1 (Ldb1) self association domain L87K

LIM domain-binding protein 1, L87K experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: LIM domain-binding protein 1, L87K dimer, 45 kDa Mus musculus protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP,, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 19
Self association of LIM domain binding protein 1, LDB1
Jacqueline Matthews
RgGuinier 2.4 nm
Dmax 7.6 nm
VolumePorod 78 nm3

SASDF89 – LIM domain-binding protein 1 (Ldb1) self association domain L87Q

LIM domain-binding protein 1, L87Q experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: LIM domain-binding protein 1, L87Q dimer, 45 kDa Mus musculus protein
Buffer: 20 mM Tris, 150 mM NaCl, 1 mM TCEP,, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2015 Nov 19
Self association of LIM domain binding protein 1, LDB1
Jacqueline Matthews
RgGuinier 2.4 nm
Dmax 7.4 nm
VolumePorod 82 nm3

SASDHD2 – Urate Oxidase (Uricase) from Aspergillus flavus, measured by SEC-SAXS

Urate Oxidase (Uricase) from Aspergillus flavus experimental SAS data
CORAL model
Sample: Urate Oxidase (Uricase) from Aspergillus flavus tetramer, 137 kDa Aspergillus flavus protein
Buffer: 20 mM Tris. 150 mM NaCl, 1 mM EDTA, 5 mM DTT, pH: 8
Experiment: SAXS data collected at BL4-2, Stanford Synchrotron Radiation Lightsource (SSRL) on 2019 Jul 1
Urate Oxidase (Uricase) from Aspergillus flavus
Tsutomu Matsui
RgGuinier 3.3 nm
Dmax 9.3 nm
VolumePorod 225 nm3

SASDJM4 – ATP-dependent DNA helicase UvrD1 (Apo-UvrD)

ATP-dependent DNA helicase UvrD1 experimental SAS data
DAMFILT model
Sample: ATP-dependent DNA helicase UvrD1 monomer, 85 kDa Mycobacterium tuberculosis protein
Buffer: 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2020 Feb 28
Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran
RgGuinier 3.4 nm
Dmax 8.4 nm
VolumePorod 132 nm3

SASDJN4 – ATP-dependent DNA helicase UvrD-ATP complex

ATP-dependent DNA helicase UvrD1 experimental SAS data
DAMFILT model
Sample: ATP-dependent DNA helicase UvrD1 monomer, 85 kDa Mycobacterium tuberculosis protein
Buffer: 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2020 Feb 28
Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran
RgGuinier 3.5 nm
Dmax 9.5 nm
VolumePorod 101 nm3

SASDMC2 – SWAXS data from Lysozyme Solution [Protein concentration 5 mg/ml] at 10 °C

Lysozyme C experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Lysozyme C monomer, 14 kDa Gallus gallus protein
Buffer: 40 mM NaOAc pH 3.8, 150 mM NaCl, pH: 3.8
Experiment: SAXS data collected at X9A, National Synchrotron Light Source (NSLS) on 2014 May 2
Visualizing how inclusion of higher reciprocal space in SWAXS data analysis improves shape restoration of biomolecules: case of lysozyme. J Biomol Struct Dyn :1-15 (2021)
Ashish
RgGuinier 1.3 nm
Dmax 4.2 nm