Browse by ORGANISM: Escherichia coli

SASDFY6 – DNA-binding protein HU-alpha, E38K/V42L double mutant bound to 80 bp DNA (ratio DNA:Protein 1:8)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E38K/V42L double mutant experimental SAS data
CHIMERA model
Sample: 80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA
80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA
DNA-binding protein HU-alpha, E38K/V42L double mutant octamer, 76 kDa Escherichia coli protein
Buffer: 50 mM Tris-HCl, 150 mM NaCl, 1 mM DTT, 1 mM PMSF, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Apr 23
Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling (supplementary)
Soumya G Remesh
RgGuinier 5.8 nm
Dmax 28.1 nm
VolumePorod 296 nm3

SASDFZ6 – DNA-binding protein HU-alpha, E38K/V42L double mutant bound to 80 bp DNA (ratio DNA:Protein 1:16)

80bp_DNA Forward80bp_DNA ReverseDNA-binding protein HU-alpha, E38K/V42L double mutant experimental SAS data
CHIMERA model
Sample: 80bp_DNA Forward monomer, 25 kDa Escherichia coli DNA
80bp_DNA Reverse monomer, 25 kDa Escherichia coli DNA
DNA-binding protein HU-alpha, E38K/V42L double mutant 16-mer, 153 kDa Linked to wild-type … protein
Buffer: 50 mM Tris-HCl, 150 mM NaCl, 1 mM DTT, 1 mM PMSF, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2015 Apr 23
Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling (supplementary)
Soumya G Remesh
RgGuinier 6.3 nm
Dmax 27.3 nm
VolumePorod 401 nm3

SASDFD5 – Tetracycline repressor (class D), TetR(D)

Tetracycline repressor (class D) experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Tetracycline repressor (class D) dimer, 47 kDa Escherichia coli protein
Buffer: 50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Sep 23
Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding. Biochim Biophys Acta Proteins Proteom :140404 (2020)
Palm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W
RgGuinier 2.6 nm
Dmax 7.7 nm
VolumePorod 85 nm3

SASDFE5 – Tetracycline repressor (class D), TetR(D), in complex with 5a,6-anhydrotetracycline (ATc)

Tetracycline repressor (class D)5a,6-anhydrotetracycline experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Tetracycline repressor (class D) dimer, 47 kDa Escherichia coli protein
5a,6-anhydrotetracycline dimer, 1 kDa
Buffer: 50 mM Tris/HCl 150 mM NaCl 10 mM MgCl2, pH: 8
Experiment: SAXS data collected at EMBL P12, PETRA III on 2013 Sep 23
Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding. Biochim Biophys Acta Proteins Proteom :140404 (2020)
Palm GJ, Buchholz I, Werten S, Girbardt B, Berndt L, Delcea M, Hinrichs W
RgGuinier 2.6 nm
Dmax 6.8 nm
VolumePorod 77 nm3

SASDEB9 – Flagellar brake protein YcgR from Escherichia coli

Flagellar brake protein YcgR experimental SAS data
SASREF model
Sample: Flagellar brake protein YcgR monomer, 29 kDa Escherichia coli protein
Buffer: 20 mM HEPES, 150mM NaCl, 10% glycerol,, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2016 Jan 4
Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli. J Biol Chem 295(3):808-821 (2020)
Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF
RgGuinier 2.6 nm
Dmax 9.1 nm
VolumePorod 44 nm3

SASDEC9 – Flagellar brake protein YcgR in complex with c-di-GMP from Escherichia coli

Flagellar brake protein YcgR in complex with c-di-GMP experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Flagellar brake protein YcgR in complex with c-di-GMP monomer, 29 kDa Escherichia coli protein
Buffer: 20 mM HEPES, 150mM NaCl, 10% glycerol,, pH: 7.5
Experiment: SAXS data collected at BL19U2, Shanghai Synchrotron Radiation Facility (SSRF) on 2016 Jan 4
Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli. J Biol Chem 295(3):808-821 (2020)
Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF
RgGuinier 2.2 nm
Dmax 7.3 nm
VolumePorod 44 nm3

SASDKE4 – Polymorphic DNA protection during starvation protein (Dps)-DNA сo-сrystals

DNA protection during starvation protein experimental SAS data
DNA protection during starvation protein Kratky plot
Sample: DNA protection during starvation protein dodecamer, 224 kDa Escherichia coli (strain … protein
Buffer: 10 mM Tris-HCl, 100 mM NaCl, 0.5 mM EDTA, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Oct 28
Polymorphic Protective Dps-DNA Co-Crystals by Cryo Electron Tomography and Small Angle X-Ray Scattering. Biomolecules 10(1) (2019)
Kamyshinsky R, Chesnokov Y, Dadinova L, Mozhaev A, Orlov I, Petoukhov M, Orekhov A, Shtykova E, Vasiliev A

SASDGV5 – The nucleotide binding domain of Lipid A export ATP-binding/permease protein MsbA - data from stop-and-flow time-resolved SAXS (12 s time course)

Lipid A export ATP-binding/permease protein MsbA - Nucleotide binding domain experimental SAS data
Lipid A export ATP-binding/permease protein MsbA - Nucleotide binding domain Kratky plot
Sample: Lipid A export ATP-binding/permease protein MsbA - Nucleotide binding domain monomer, 27 kDa Escherichia coli protein
Buffer: 20 mM Tris, 150 mM NaCl, 5 mM MgCl2, 0.45 mM Mg2+-ATP, pH: 7.5
Experiment: SAXS data collected at EMBL P12, PETRA III on 2017 Dec 8
Structural Kinetics of MsbA Investigated by Stopped-Flow Time-Resolved Small-Angle X-Ray Scattering. Structure (2019)
Josts I, Gao Y, Monteiro DCF, Niebling S, Nitsche J, Veith K, Gräwert TW, Blanchet CE, Schroer MA, Huse N, Pearson AR, Svergun DI, Tidow H
RgGuinier 2.1 nm
Dmax 6.8 nm
VolumePorod 50 nm3

SASDE52 – Ribonuclease E from Escherichia coli

Endoribonuclease E experimental SAS data
DAMFILT model
Sample: Endoribonuclease E tetramer, 247 kDa Escherichia coli protein
Buffer: 10 mM DTT, 10 mM MgCl2, 0.5 M NaCl, 20 mM Tris, pH: 8
Experiment: SAXS data collected at B21, Diamond Light Source on 2017 Feb 11
A structural and biochemical comparison of Ribonuclease E homologues from pathogenic bacteria highlights species-specific properties. Sci Rep 9(1):7952 (2019)
Mardle CE, Shakespeare TJ, Butt LE, Goddard LR, Gowers DM, Atkins HS, Vincent HA, Callaghan AJ
RgGuinier 5.0 nm
Dmax 16.1 nm
VolumePorod 468 nm3

SASDFZ3 – Escherichia coli YjhC

Escherichia coli YjhC experimental SAS data
PDB (PROTEIN DATA BANK) model
Sample: Escherichia coli YjhC dimer, 86 kDa Escherichia coli protein
Buffer: 20 mM Tris, 150 mM NaCl, 0.1 % (w/v) sodium azide, 5 % (v/v) glycerol, pH: 8
Experiment: SAXS data collected at SAXS/WAXS, Australian Synchrotron on 2018 Apr 12
On the structure and function of Escherichia coli YjhC: an oxidoreductase involved in bacterial sialic acid metabolism. Proteins (2019)
Horne CR, Kind L, Davies JS, Dobson RCJ
RgGuinier 3.1 nm
Dmax 10.7 nm
VolumePorod 130 nm3