1i6l
From Proteopedia
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|PDB= 1i6l |SIZE=350|CAPTION= <scene name='initialview01'>1i6l</scene>, resolution 1.72Å | |PDB= 1i6l |SIZE=350|CAPTION= <scene name='initialview01'>1i6l</scene>, resolution 1.72Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TYM:TRYPTOPHANYL-5'AMP'>TYM</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1i6k|1I6K]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i6l OCA], [http://www.ebi.ac.uk/pdbsum/1i6l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1i6l RCSB]</span> | ||
}} | }} | ||
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[[Category: Carter, C W.]] | [[Category: Carter, C W.]] | ||
[[Category: Retailleau, P.]] | [[Category: Retailleau, P.]] | ||
| - | [[Category: GOL]] | ||
| - | [[Category: NH4]] | ||
| - | [[Category: SO4]] | ||
| - | [[Category: TYM]] | ||
[[Category: aar]] | [[Category: aar]] | ||
[[Category: class i trna synthetase]] | [[Category: class i trna synthetase]] | ||
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[[Category: trpr]] | [[Category: trpr]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:15:15 2008'' |
Revision as of 18:15, 30 March 2008
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| , resolution 1.72Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Activity: | Tryptophan--tRNA ligase, with EC number 6.1.1.2 | ||||||
| Related: | 1I6K
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP
Overview
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.
About this Structure
1I6L is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.
Reference
High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP., Retailleau P, Yin Y, Hu M, Roach J, Bricogne G, Vonrhein C, Roversi P, Blanc E, Sweet RM, Carter CW Jr, Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1595-608. Epub, 2001 Oct 25. PMID:11679724
Page seeded by OCA on Sun Mar 30 21:15:15 2008
