Primary Citation PubMed: 15711564
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Evaluation of the structural quality of modeled proteins by using globularity criteria.
(2007) BMC Struct Biol 7
PubMed: 17346357 | PubMedCentral: PMC1828058 | DOI: 10.1186/1472-6807-7-9
Following these criteria thirteen targets were selected, i.e. T0198 (PDB code: 1SUM (3–223)) and T0238 (1W33 (70–222)) classified as "mainly-alpha", T0212 (1TZA (3–121)) and T0... 09_1 (1XQB (9–138)) as "mainly-beta", T0199_3 (1STZ (145–226)), T0201 (1S12 (1–90)), T0209_2 (1XQB(159–221), T0216_1 (1VL4(2–214)), T0216_2 (1VL4(221–433)), T0239 (1RKI(1–98)) and T0248_2 (1TD6 (107–193)) as "alpha+beta" and T0242 (2BLK (2–116)) and T0273 (1WDJ(2–187)) as "alpha/beta".
Publication Year: 2007
Further structural insights into the binding of complement factor H by complement regulator-acquiring surface protein 1 (CspA) of Borrelia burgdorferi.
(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69
PubMed: 23722839 | PubMedCentral: PMC3668580 | DOI: 10.1107/S1744309113012748
Structure determination and refinement The structure was solved in space group C 2 by molecular replacement using the existing CspA structure (PDB entry 1w33 chain A ; Cordes et al.... , 2005 ▶ ) and Phaser (McCoy et al. , 2007 ▶ ) from the CCP 4 suite (Winn et al. , 2011 ▶ ).
Figure 2 Comparison between PDB entries 4bl4 and 1w33 .
( e ) Overlay of the dimer assemblies found in 1w33 and 4bl4 , showing the difference in the intermonomer angle.
( a , b ) Surface representations of dimers from PDB entries 1w33 and 4bl4 , respectively, highlighting residues Lys136, Lys141, Lys143, Glu144 and Glu47 which have been shown to be involved in factor H/FHL-1 binding (Kraiczy et al. , 2009 ▶ ).
Measurement of the difference in inter-domain angles between PDB entries 4bl4 and 1w33 was performed using secondary-structure matching over residues 70–220 with LSQKAB (Kabsch, 1976 ▶ ).
( a ) Cartoon representation of the structure of the CspA dimer found in PDB entry 1w33 .
Chains A from 1w33 (grey) and 4bl4 (red) were superposed using secondary-structure matching over residues 70–220.
of molecules in unit cell Z 16 Matthews coefficient V M ( 3 Da 1 ) 2.75 Solvent content (%) 53.3 Resolution () 93.264.06 (4.164.06) R merge 0.194 (0.596) I /( I ) 5.7 (2.7) Completeness (%) 95.9 (98.6) Multiplicity 3.7 (3.7) Data-processing software xia 2 Phasing method Molecular replacement Search model 1w33 chain A Solution software Phaser Table 2 Structure refinement and model validation Values in parentheses are for the highest resolution shell.
( b ) Superposition (r.m.s.d. = 0.138 Å) of C-terminal residues 230–250 from chain A in 4bl4 (red) and 1w33 (blue) shown as a cartoon against chain B rendered as a surface (grey).
Comparing the conformation of both copies of the dimer in the asymmetric unit with that in PDB entry 1w33 shows that the angle between the subunits has increased by an average of 16.8° (Fig. 2 ▶ ).
The average r.m.s.d. of superposition of each chain in 1w33 onto each chain in 4bl4 over this residue range is 0.539 Å.
( d ) Subunits from 1w33 (blue) and 4bl4 (red) superposed, showing the deflection of helix F between residues 225 and 227 (shown in yellow).
( f ) Superposition of C-terminal residues from chain A of 1w33 and 4bl4 , showing an average increase in intermonomer angle of 16.8° averaged over both copies of the dimer in the 4bl4 asymmetric unit (the individual angles for the AB and CD dimers are 16.96 and 16.66°, respectively).
Publication Year: 2013
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