This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1i6l
From Proteopedia
| Line 4: | Line 4: | ||
|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> | ||
}} | }} | ||
| Line 25: | Line 28: | ||
[[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]] | ||
| Line 34: | Line 33: | ||
[[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
| |||||||
| , 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
