3chb
From Proteopedia
(New page: 200px<br /><applet load="3chb" size="450" color="white" frame="true" align="right" spinBox="true" caption="3chb, resolution 1.25Å" /> '''CHOLERA TOXIN B-PENT...) |
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| - | [[Image:3chb.gif|left|200px]]<br /><applet load="3chb" size=" | + | [[Image:3chb.gif|left|200px]]<br /><applet load="3chb" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="3chb, resolution 1.25Å" /> | caption="3chb, resolution 1.25Å" /> | ||
'''CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE'''<br /> | '''CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Crystals of the 61 kDa complex of the cholera toxin B-pentamer with the | + | Crystals of the 61 kDa complex of the cholera toxin B-pentamer with the ganglioside GM1 receptor pentasaccharide diffract to near-atomic resolution. We have refined the crystallographic model for this complex using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.129 for all observed Bragg reflections in the resolution range 22 A to 1.25 A. Remarkably few residues show evidence of discrete conformational disorder. A notable exception is a minority conformation found for the Cys9 side-chain, which implies that the Cys9-Cys86 disulfide linkage is incompletely formed. In all five crystallographically independent instances, the peptide backbone in the region of the receptor-binding site shows evidence of strain, including unusual bond lengths and angles, and a highly non-planar (omega=153.7(7) degrees) peptide group between residues Gln49 and Val50. The location of well-ordered water molecules at the protein surface is notable reproduced among the five crystallographically independent copies of the peptide chain, both at the receptor-binding site and elsewhere. The 5-fold non-crystallographic symmetry of this complex allows an evaluation of the accuracy, reproducibility, and derived error estimates from refinement of large structures at near-atomic resolution. We find that blocked-matrix treatment of parameter covariance underestimates the uncertainty of atomic positions in the final model by approximately 10% relative to estimates based either on full-matrix inversion or on the 5-fold non-crystallographic symmetry. |
==About this Structure== | ==About this Structure== | ||
| - | 3CHB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae] with UNX and MES as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 3CHB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae] with <scene name='pdbligand=UNX:'>UNX</scene> and <scene name='pdbligand=MES:'>MES</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CHB OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Vibrio cholerae]] | [[Category: Vibrio cholerae]] | ||
| - | [[Category: Hol, W | + | [[Category: Hol, W G.J.]] |
| - | [[Category: Merritt, E | + | [[Category: Merritt, E A.]] |
[[Category: MES]] | [[Category: MES]] | ||
[[Category: UNX]] | [[Category: UNX]] | ||
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[[Category: toxin/receptor complex]] | [[Category: toxin/receptor complex]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:08:44 2008'' |
Revision as of 17:08, 21 February 2008
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CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE
Overview
Crystals of the 61 kDa complex of the cholera toxin B-pentamer with the ganglioside GM1 receptor pentasaccharide diffract to near-atomic resolution. We have refined the crystallographic model for this complex using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.129 for all observed Bragg reflections in the resolution range 22 A to 1.25 A. Remarkably few residues show evidence of discrete conformational disorder. A notable exception is a minority conformation found for the Cys9 side-chain, which implies that the Cys9-Cys86 disulfide linkage is incompletely formed. In all five crystallographically independent instances, the peptide backbone in the region of the receptor-binding site shows evidence of strain, including unusual bond lengths and angles, and a highly non-planar (omega=153.7(7) degrees) peptide group between residues Gln49 and Val50. The location of well-ordered water molecules at the protein surface is notable reproduced among the five crystallographically independent copies of the peptide chain, both at the receptor-binding site and elsewhere. The 5-fold non-crystallographic symmetry of this complex allows an evaluation of the accuracy, reproducibility, and derived error estimates from refinement of large structures at near-atomic resolution. We find that blocked-matrix treatment of parameter covariance underestimates the uncertainty of atomic positions in the final model by approximately 10% relative to estimates based either on full-matrix inversion or on the 5-fold non-crystallographic symmetry.
About this Structure
3CHB is a Single protein structure of sequence from Vibrio cholerae with and as ligands. Full crystallographic information is available from OCA.
Reference
The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site., Merritt EA, Kuhn P, Sarfaty S, Erbe JL, Holmes RK, Hol WG, J Mol Biol. 1998 Oct 9;282(5):1043-59. PMID:9753553
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