1I6K

1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP

Summary for 1I6K

• Entry DOI: 10.2210/pdb1i6k/pdb
• Descriptor: TRYPTOPHANYL-TRNA SYNTHETASE, SULFATE ION, AMMONIUM ION, ... (6 entities in total)
• Functional Keywords: class i trna synthetase, aars, induced fit, trprs, ligase
• Biological source: Geobacillus stearothermophilus
• Cellular location: Cytoplasm: P00953
• Total number of polymer chains: 1
• Total formula weight: 39286.91

Authors

Retailleau, P.,Carter, C.W. (deposition date: 2001-03-02, release date: 2001-11-07, Last modification date: 2024-10-30)

Primary citation

Retailleau, P.,Yin, Y.,Hu, M.,Roach, J.,Bricogne, G.,Vonrhein, C.,Roversi, P.,Blanc, E.,Sweet, R.M.,Carter, C.W.
High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP.
Acta Crystallogr.,Sect.D, 57:1595-1608, 2001

PubMed Abstract: Native data, anomalous data at three wavelengths and an independent peak-wavelength data set for SeMet-substituted protein have been collected from cryoprotected crystals of the TrpRS-adenylate product (TAM) complex to a resolution limit of 1.7 A. Independent phase sets were developed using SHARP and improved by solvent flipping with SOLOMON using molecular envelopes derived from experimental densities for, respectively, peak-wavelength SAD data from four different crystals, MAD data and their M(S)IRAS combinations with native data. Hendrickson-Lattman phase-probability coefficients from each phase set were used in BUSTER to drive maximum-likelihood refinements of well defined parts of the previously refined room-temperature 2.9 A structure. Maximum-entropy completion followed by manual rebuilding was then used to generate a model for the missing segments, bound ligand and solvent molecules. Surprisingly, peak-wavelength SAD experiments produced the smallest phase errors relative to the refined structures. Selenomethionylated models deviate from one another by 0.25 A and from the native model by 0.38 A, but all have r.m.s. deviations of approximately 1.0 A from the 2.9 A model. Difference Fourier calculations between amplitudes from the 300 K experiment and the new amplitudes at 100 K using 1.7 A model phases show no significant structural changes arising from temperature variation or addition of cryoprotectant. The main differences between low- and high-resolution structures arise from correcting side-chain rotamers in the core of the protein as well as on the surface. These changes improve various structure-validation criteria.

PubMed: 11679724
DOI: 10.1107/S090744490101215X

Experimental method

X-RAY DIFFRACTION (1.72 Å)