| Literature DB >> 27658298 |
Kayode K Ojo, Ranae M Ranade, Zhongsheng Zhang, David M Dranow, Janette B Myers, Ryan Choi, Steve Nakazawa Hewitt, Thomas E Edwards, Douglas R Davies, Donald Lorimer, Stephen M Boyle, Lynn K Barrett, Frederick S Buckner, Erkang Fan, Wesley C Van Voorhis.
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0160350.].Entities:
Year: 2016 PMID: 27658298 PMCID: PMC5033446 DOI: 10.1371/journal.pone.0163641
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Fig 7A superposition of BmMetRS (PDB ID 4PY2 Chain B) and TbMetRS (PDB ID 4MVW Chain) bound to compound 1433.
A key difference is the interaction of BmMetRS Phe213 which is functionally equivalent to Leu456 in TbMetRS but led to different protein geometry. The TbMetRS structure is shown in blue and the 2 different residues in orange.
Data collection and model refinement statistics.
| Crystal | SeMet | 1312 | 1415 | 1433 |
|---|---|---|---|---|
| PDB code | 4DLP | 5K0S | 5K0T | 4PY2 |
| Data collection | ||||
| Space Group | P 1 21 1 | P 1 | P 1 | P 1 |
| Cell dimensions | ||||
| 116.25, 77.62, 116.27 | 45.27, 99.74, 104.63 | 45.16, 99.65, 104.30 | 45.01, 99.48, 104.00 | |
| Α, β, γ (°) | 90, 119.67, 90 | 110.58, 87.63, 99.91 | 110.46, 88.09, 99.72 | 110.47, 87.24, 99.99 |
| Resolution range (Å) | 50.00–2.65 (2.72–2.65) | 50.00–2.40 (2.46–2.40) | 50.00–2.60 (2.67–2.60) | 50.00–2.15 (2.21–2.15) |
| No. of unique reflections | 52379 | 63652 | 49660 | 88924 |
| Rmerge (%)a | 7.1 (48.6) | 6.4 (52.5) | 7.5 (47.0) | 6.6 (53.6) |
| Redudancy a | 3.7 (3.7) | 2.4 (2.4) | 2.4 (2.4) | 3.9 (4.0) |
| Completeness (%)a | 99.3 (99.5) | 96.3 (85.2) | 96.0 (97.5) | 98.2 (97.3) |
| l/σIa | 15.21 (2.63) | 11.43 (2.13) | 10.12 (2.07) | 15.76 (2.73) |
| Refinement | ||||
| Resolution range | 50.00–2.65 (2.72–2.65) | 50.00–2.40 (2.46–2.40) | 50.00–2.60 (2.67–2.60) | 50.00–2.15 (2.21–2.15) |
| No. of protein atoms | 10934 | 11469 | 11189 | 11480 |
| No. of water molecules | 88 | 219 | 169 | 135 |
| 19.7 | 21.0 | 25.6 | 17.8 | |
| 23.7 | 25.6 | 28.6 | 21.1 | |
| Root-mean-square deviations from ideal stereochemistry | ||||
| Bond lengths (Å) | 0.012 | 0.003 | 0.008 | 0.011 |
| Bond angles (°) | 1.421 | 0.577 | 1.183 | 1.384 |
| Mean B factor (all atoms) (Å2) | 48.25 | 43.29 | 49.76 | 35.98 |
| Ramachandran plot | ||||
| Favored region (%) | 96.87 | 98.77 | 98.67 | 97.43 |
| Allowed regions (%) | 3.13 | 1.23 | 1.33 | 2.57 |
| Outlier regions (%) | 0.00 | 0.00 | 0.00 | 0.00 |
| Clashscore | 2.3 | 2.5 | 0.46 | 0.79 |
| Molprobity Score | 1.18 | 1.15 | 0.74 | 0.75 |