3DV4

Crystal structure of SAG506-01, tetragonal, crystal 1

Summary for 3DV4

• Entry DOI: 10.2210/pdb3dv4/pdb
• Related: 3DUR 3DUS 3DUU 3DV6
• Descriptor: antibody Fv fragment SAG506-01, Ig-like protein, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: antibody, kdo, twinning, pseudo-symmetry, immune system
• Biological source: Mus Musculus (mouse); More
• Total number of polymer chains: 2
• Total formula weight: 26253.56

Authors

Brooks, C.L.,Blackler, R.J.,Gerstenbruch, S.,Kosma, P.,Muller-Loennies, S.,Brade, H.,Evans, S.V. (deposition date: 2008-07-18, release date: 2008-12-02, Last modification date: 2024-10-30)

Primary citation

Brooks, C.L.,Blackler, R.J.,Gerstenbruch, S.,Kosma, P.,Muller-Loennies, S.,Brade, H.,Evans, S.V.
Pseudo-symmetry and twinning in crystals of homologous antibody Fv fragments.
Acta Crystallogr.,Sect.D, 64:1250-1258, 2008

PubMed Abstract: A difference of seven conservative amino-acid substitutions between two single-chain antibodies (scFvs) specific for chlamydial lipopolysaccharide does not significantly affect their molecular structures or packing contacts, but dramatically affects their crystallization. The structure of the variable domain (Fv) of SAG173-04 was solved to 1.86 A resolution and an R(cryst) of 18.9% in space group P2(1)2(1)2(1). Crystals of the homologous SAG506-01 diffracted to 1.95 A resolution and appeared at first to have Patterson symmetry I4/m or P4/mmm; however, no solution could be found in space groups belonging to the former and refinement in the only solution corresponding to the latter (in space group P4(3)2(1)2) stalled at R(free) = 30.0%. Detailed examination of the diffraction data revealed that the crystal was likely to be twinned and that the correct space group was P2(1)2(1)2(1). Both translational pseudo-symmetry and pseudo-merohedral twinning were observed in one crystal of SAG506-01 and pseudo-merohedral twinning was observed for a second crystal. The final R factor for SAG506-01 after refinement in P2(1)2(1)2(1) was 20.5%.

PubMed: 19018101
DOI: 10.1107/S0907444908033453

Experimental method

X-RAY DIFFRACTION (1.95 Å)