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1SX2

Use of a Halide Binding Site to Bypass the 1000-atom Limit to Structure Determination by Direct Methods

Summary for 1SX2
Entry DOI10.2210/pdb1sx2/pdb
Related1SWY 1SWZ 1SX7
DescriptorLysozyme, RUBIDIUM ION, CHLORIDE ION, ... (5 entities in total)
Functional Keywordsrb+ binding sites; ab initio direct methods, hydrolase
Biological sourceEnterobacteria phage T4
Cellular locationHost cytoplasm : P00720
Total number of polymer chains1
Total formula weight19351.25
Authors
Mooers, B.H.M.,Matthews, B.W. (deposition date: 2004-03-30, release date: 2004-11-23, Last modification date: 2024-02-14)
Primary citationMooers, B.H.,Matthews, B.W.
Use of an ion-binding site to bypass the 1000-atom limit to structure determination by direct methods.
Acta Crystallogr.,Sect.D, 60:1726-1737, 2004
Cited by
PubMed Abstract: Proteins with more than 1000 non-H atoms and without heavy-atom prosthetic groups are very difficult to solve by ab initio direct methods. T4 lysozyme is being used to explore these limits. The protein has 1309 non-H atoms, seven S atoms, no disulfide bonds and no heavy-atom prosthetic group. It is recalcitrant to structure determination by direct methods using X-ray diffraction data to 0.97 A. It is shown here that it is possible to obtain a truly ab initio structure determination of a variant of the protein that has an Rb+ (Z = 37) binding site. Using diffraction data to 1.06 A resolution, the direct-methods programs SIR2002 and ACORN independently solved the structure in about 20 h. The bound Rb+, which contributes about 1.7% of the total scattering, does not appear to distort the structure or to inhibit refinement (R factor 12.1%). The phases obtained via SIR2002 or ACORN are in good agreement with those from a reference structure obtained from conventional molecular-substitution and refinement procedures (average error in the figure-of-merit-weighted phases of less than 25 degrees). Thus, proteins with more than 1000 atoms that include halide-binding or other such sites may be amenable to structure determination by ab initio direct methods. The direct-methods approaches are also compared with structure determination via use of the anomalous scattering of the Rb+ ion. As shown by examples, high-resolution structures determined by direct methods can be useful in highlighting regions of strain in the protein, including short hydrogen bonds and non-planar peptide groups.
PubMed: 15388918
DOI: 10.1107/S0907444904017020
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.06 Å)
Structure validation

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