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sopb gene, encoding the full-length (fl) sopb protein  (GenScript corporation)

 
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    Structured Review

    GenScript corporation sopb gene, encoding the full-length (fl) sopb protein
    Selected crystallographic data for <t> SopB–DNA </t> structures
    Sopb Gene, Encoding The Full Length (Fl) Sopb Protein, supplied by GenScript corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/sopb+gene%2C+encoding+the+full-length+%28fl%29+sopb+protein/pmc02910045-92-6-20?v=GenScript+corporation
    Average 90 stars, based on 1 article reviews
    sopb gene, encoding the full-length (fl) sopb protein - by Bioz Stars, 2026-07
    90/100 stars

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    1) Product Images from "Insight into F plasmid DNA segregation revealed by structures of SopB and SopB–DNA complexes"

    Article Title: Insight into F plasmid DNA segregation revealed by structures of SopB and SopB–DNA complexes

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkq161

    Selected crystallographic data for SopB–DNA structures
    Figure Legend Snippet: Selected crystallographic data for SopB–DNA structures

    Techniques Used:

    Selected crystallographic data for SopB(275–323)
    Figure Legend Snippet: Selected crystallographic data for SopB(275–323)

    Techniques Used:

    Crystal structures of SopB-18mer complexes. ( A ) A section of the experimental MAD electron density map (shown as a blue mesh) for the FL SopB-18mer complex, contoured at 1.5σ and calculated to 3.5 Å resolution. Labeled are the location of the pseudocontinuous DNA and one of the SopB intermolecular dimers, which bridge between DNA duplexes to form the crystal lattice. Also labeled is one of the large solvent channels. ( B ) Ribbon diagram of the I23 SopB-18mer complex. The crystallographic asymmetric unit (ASU) consists of two subunits (cyan and magenta) and one 18-mer DNA duplex. Shown also are subunits involved in secondary dimer/bridging interactions, generated in the crystals. For the cyan subunit, the secondary structural elements are labeled and the first and last residues observed in the structure are labeled N and C, respectively. This figure ( C and D ) and Figures 2A–D, 3, 4, 5A and C, and 6A and B were made with PyMOL (55). (C) Ribbon diagram of the P3 1 21 SopB(155–272)-18mer complex. The molecules in the ASU are all shown consisting of three SopB secondary dimers and four 18mer duplexes, which all pack pseudocontinuously in the crystal. The specific HTH-major groove interacting subunits are labeled canonical major groove and the one subunit that interacts non-specifically with two minor grooves (colored blue) is also shown and its minor groove contacts labeled. (D) Ribbon diagram of the P2 1 SopB(155–272)-18mer complex. The ASU consists of one secondary dimer and two SopB subunits and two 18-mer DNA duplexes.
    Figure Legend Snippet: Crystal structures of SopB-18mer complexes. ( A ) A section of the experimental MAD electron density map (shown as a blue mesh) for the FL SopB-18mer complex, contoured at 1.5σ and calculated to 3.5 Å resolution. Labeled are the location of the pseudocontinuous DNA and one of the SopB intermolecular dimers, which bridge between DNA duplexes to form the crystal lattice. Also labeled is one of the large solvent channels. ( B ) Ribbon diagram of the I23 SopB-18mer complex. The crystallographic asymmetric unit (ASU) consists of two subunits (cyan and magenta) and one 18-mer DNA duplex. Shown also are subunits involved in secondary dimer/bridging interactions, generated in the crystals. For the cyan subunit, the secondary structural elements are labeled and the first and last residues observed in the structure are labeled N and C, respectively. This figure ( C and D ) and Figures 2A–D, 3, 4, 5A and C, and 6A and B were made with PyMOL (55). (C) Ribbon diagram of the P3 1 21 SopB(155–272)-18mer complex. The molecules in the ASU are all shown consisting of three SopB secondary dimers and four 18mer duplexes, which all pack pseudocontinuously in the crystal. The specific HTH-major groove interacting subunits are labeled canonical major groove and the one subunit that interacts non-specifically with two minor grooves (colored blue) is also shown and its minor groove contacts labeled. (D) Ribbon diagram of the P2 1 SopB(155–272)-18mer complex. The ASU consists of one secondary dimer and two SopB subunits and two 18-mer DNA duplexes.

    Techniques Used: Labeling, Solvent, Generated

    Structure of SopB(275–323) dimer-domain. ( A ) Left, a section of the experimental MIR electron density map for the SopB(275–323) structure (blue mesh) contoured at 1σ. Right, ribbon diagram of the SopB(275–323) structure with one subunit colored red and labeled, and the other subunit colored green. ( B ) Comparison of the P1 ParB dimer-domain–DNA complex (right) with the corresponding SopB dimer-domain (left). Note that although the overall structure and topology are similar, P1 ParB has extended loops between its β1–β2 and β2–β3 units that are responsible for DNA binding that are not present in SopB. ( C ) Comparison of the electrostatic surfaces of the P1 ParB and SopB. Shown is the helical containing face of each dimer-domain, which is strongly electronegative (red) in both structures. ( D ) Electrostatic surface of the face opposite to that shown in (C). This face, which is involved in DNA-binding in the P1 ParB protein, is electropositive (blue) in each structure.
    Figure Legend Snippet: Structure of SopB(275–323) dimer-domain. ( A ) Left, a section of the experimental MIR electron density map for the SopB(275–323) structure (blue mesh) contoured at 1σ. Right, ribbon diagram of the SopB(275–323) structure with one subunit colored red and labeled, and the other subunit colored green. ( B ) Comparison of the P1 ParB dimer-domain–DNA complex (right) with the corresponding SopB dimer-domain (left). Note that although the overall structure and topology are similar, P1 ParB has extended loops between its β1–β2 and β2–β3 units that are responsible for DNA binding that are not present in SopB. ( C ) Comparison of the electrostatic surfaces of the P1 ParB and SopB. Shown is the helical containing face of each dimer-domain, which is strongly electronegative (red) in both structures. ( D ) Electrostatic surface of the face opposite to that shown in (C). This face, which is involved in DNA-binding in the P1 ParB protein, is electropositive (blue) in each structure.

    Techniques Used: Labeling, Comparison, Binding Assay

    SopB primary and secondary (bridging) dimers. Relationship of the SopB primary and secondary dimers. The structure of the SopB primary dimer bound to the palindromic DNA site was produced by combining the DNA-binding and dimer-domains (the flexible linkage is indicated by dashed lines). Above is shown the secondary dimer contacts that permit SopB to bridge or spread between multiple, adjacent DNA sites (generated by a 90° rotation).
    Figure Legend Snippet: SopB primary and secondary (bridging) dimers. Relationship of the SopB primary and secondary dimers. The structure of the SopB primary dimer bound to the palindromic DNA site was produced by combining the DNA-binding and dimer-domains (the flexible linkage is indicated by dashed lines). Above is shown the secondary dimer contacts that permit SopB to bridge or spread between multiple, adjacent DNA sites (generated by a 90° rotation).

    Techniques Used: Produced, Binding Assay, Generated

    The SopB α6–α7 secondary dimer interactions. ( A ) Ribbon diagram showing the residues that are involved in the formation of the secondary dimer interaction. Two views are included that are related by a ∼90° rotation. Residues that contribute to the interface are shown as sticks and labeled. Also labeled are α6 and α7. ( B ) Superimposition of subunits of all the secondary dimers reveals that the dimerization is not symmetric but mediated by one subunit making one set of contacts and the other making a different set of contacts. This asymmetric arrangement is observed in all dimers.
    Figure Legend Snippet: The SopB α6–α7 secondary dimer interactions. ( A ) Ribbon diagram showing the residues that are involved in the formation of the secondary dimer interaction. Two views are included that are related by a ∼90° rotation. Residues that contribute to the interface are shown as sticks and labeled. Also labeled are α6 and α7. ( B ) Superimposition of subunits of all the secondary dimers reveals that the dimerization is not symmetric but mediated by one subunit making one set of contacts and the other making a different set of contacts. This asymmetric arrangement is observed in all dimers.

    Techniques Used: Labeling

    SopB–DNA interactions. ( A ) Left, schematic representation of SopB–DNA interactions. Only one half site of the 18-mer duplex is shown as the identical contacts are made to each half site. The strands are labeled 1–9 and 1′–9′ (where ′ indicates other strand of the duplex). Bases are represented as rectangles and labeled according to sequence. The ribose groups are shown as pentagons. Hydrophobic contacts are indicated by lines and hydrogen bonds, by arrows. Right, close up of the SopB–DNA specific major groove interactions that are made to each half site and indicated schematically. Interacting residues are shown as blue sticks and the secondary-structural elements are labeled. ( B ) Fluorescence polarization DNA-binding isotherms comparing SopB binding to the 43- and 18-mer centromere sites. Each data set was normalized, and normalized polarizations were plotted along the y -axis against the protein concentrations, which are plotted along the x -axis. ( C ) Close up of the triple bridging interaction that is comprised of specific and non-specific SopB–DNA found in the P3 1 21 crystal form. Specifically, this dimer is the one that is also colored blue and magenta in C. The blue subunit makes non-specific minor groove contacts to two DNA duplexes while the magenta subunit makes the canonical major groove contacts indicated in A and found in all the subunits of the crystals except the P3 1 21 blue subunit.
    Figure Legend Snippet: SopB–DNA interactions. ( A ) Left, schematic representation of SopB–DNA interactions. Only one half site of the 18-mer duplex is shown as the identical contacts are made to each half site. The strands are labeled 1–9 and 1′–9′ (where ′ indicates other strand of the duplex). Bases are represented as rectangles and labeled according to sequence. The ribose groups are shown as pentagons. Hydrophobic contacts are indicated by lines and hydrogen bonds, by arrows. Right, close up of the SopB–DNA specific major groove interactions that are made to each half site and indicated schematically. Interacting residues are shown as blue sticks and the secondary-structural elements are labeled. ( B ) Fluorescence polarization DNA-binding isotherms comparing SopB binding to the 43- and 18-mer centromere sites. Each data set was normalized, and normalized polarizations were plotted along the y -axis against the protein concentrations, which are plotted along the x -axis. ( C ) Close up of the triple bridging interaction that is comprised of specific and non-specific SopB–DNA found in the P3 1 21 crystal form. Specifically, this dimer is the one that is also colored blue and magenta in C. The blue subunit makes non-specific minor groove contacts to two DNA duplexes while the magenta subunit makes the canonical major groove contacts indicated in A and found in all the subunits of the crystals except the P3 1 21 blue subunit.

    Techniques Used: Labeling, Sequencing, Fluorescence, Binding Assay

    Electrostatic surface representations of SopB-18mer specific and non-specific complexes. ( A ) SopB dimers are shown as surface representations with electropositive regions colored blue and electronegative regions red. The DNA is shown as sticks. Shown is the specific complex in which the DNA major grooves are contacted by the basic HTH motifs. ( B ) Electrostatic surface representation of the non-specific SopB–DNA complex. In this complex, the SopB secondary dimer bridges three different DNA duplexes by making non-specific contacts to the minor grooves of two DNA duplexes (from one subunit) and specific contacts to the major groove by the HTH of the second subunit.
    Figure Legend Snippet: Electrostatic surface representations of SopB-18mer specific and non-specific complexes. ( A ) SopB dimers are shown as surface representations with electropositive regions colored blue and electronegative regions red. The DNA is shown as sticks. Shown is the specific complex in which the DNA major grooves are contacted by the basic HTH motifs. ( B ) Electrostatic surface representation of the non-specific SopB–DNA complex. In this complex, the SopB secondary dimer bridges three different DNA duplexes by making non-specific contacts to the minor grooves of two DNA duplexes (from one subunit) and specific contacts to the major groove by the HTH of the second subunit.

    Techniques Used:



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