The DOI matches its Crossref record.
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
Abstract
A single protein crystal structure contains information about dynamic properties of the protein as well as providing a static view of one three-dimensional conformation. This additional information is to be found in the distribution of observed electron density about the mean position of each atom. It is general practice to account for this by refining a separate atomic displacement parameter (ADP) for each atomic center. However, these same displacements are often described well by simpler models based on TLS (translation/libration/screw) rigid-body motion of large groups of atoms, for example interdomain hinge motion. A procedure, TLSMD, has been developed that analyzes the distribution of ADPs in a previously refined protein crystal structure in order to generate optimal multi-group TLS descriptions of the constituent protein chains. TLSMD is applicable to crystal structures at any resolution. The models generated by TLSMD analysis can significantly improve the standard crystallographic residuals R and R(free) and can reveal intrinsic dynamic properties of the protein.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
Towards automated crystallographic structure refinement with phenix.refine
Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H., & Adams, P. D. (2012) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444912001308 · Cited by 5,511
Mechanism of auxin perception by the TIR1 ubiquitin ligase
Tan, X., Calderon-Villalobos, L. I. A., Sharon, M., Zheng, C., Robinson, C. V., Estelle, M., & Zheng, N. (2007) · Nature · doi:10.1038/nature05731 · Cited by 1,688
Design of protein-binding proteins from the target structure alone
Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature · doi:10.1038/s41586-022-04654-9 · Cited by 577
Structure and control of the actin regulatory WAVE complex
Chen, Z., Borek, D., Padrick, S. B., Gomez, T. S., Metlagel, Z., Ismail, A. M., Umetani, J., Billadeau, D. D., Otwinowski, Z., & Rosen, M. K. (2010) · Nature · doi:10.1038/nature09623 · Cited by 500
Fletcher, J. M., Boyle, A. L., Bruning, M., Bartlett, G. J., Vincent, T. L., Zaccai, N. R., Armstrong, C. T., Bromley, E. H. C., Booth, P. J., Brady, R. L., et al. (2012) · ACS Synthetic Biology · doi:10.1021/sb300028q · Cited by 262
The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex
Halbach, F., Reichelt, P., Rode, M., & Conti, E. (2013) · Cell · doi:10.1016/j.cell.2013.07.017 · Cited by 210
Du, X., Volkov, O. A., Czerwinski, R. M., Tan, H., Huerta, C., Morton, E. R., Rizzi, J. P., Wehn, P. M., Xu, R., Nijhawan, D., et al. (2019) · Structure · doi:10.1016/j.str.2019.10.005 · Cited by 181
Coupling of receptor conformation and ligand orientation determine graded activity
Bruning, J. B., Parent, A. A., Gil, G., Zhao, M., Nowak, J., Pace, M. C., Smith, C. L., Afonine, P. V., Adams, P. D., Katzenellenbogen, J. A., et al. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.451 · Cited by 142
Heras, B., Totsika, M., Peters, K. M., Paxman, J. J., Gee, C. L., Jarrott, R. J., Perugini, M. A., Whitten, A. E., & Schembri, M. A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1311592111 · Cited by 141
Krajewski, W. W., Collins, R., Holmberg-Schiavone, L., Jones, T. A., Karlberg, T., & Mowbray, S. L. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.10.029 · Cited by 135
A New Class of Multimerization Selective Inhibitors of HIV-1 Integrase
Sharma, A., Slaughter, A., Jena, N., Feng, L., Kessl, J. J., Fadel, H. J., Malani, N., Male, F., Wu, L., Poeschla, E., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004171 · Cited by 124
The hit-and-return system enables efficient time-resolved serial synchrotron crystallography
Schulz, E. C., Mehrabi, P., Müller-Werkmeister, H. M., Tellkamp, F., Jha, A., Stuart, W., Persch, E., De Gasparo, R., Diederich, F., Pai, E. F., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0180-2 · Cited by 111
Structural evidence for Scc4-dependent localization of cohesin loading
Hinshaw, S. M., Makrantoni, V., Kerr, A., Marston, A. L., & Harrison, S. C. (2015) · eLife · doi:10.7554/elife.06057 · Cited by 78
Watterson, D. M., Grum-Tokars, V. L., Roy, S. M., Schavocky, J. P., Bradaric, B. D., Bachstetter, A. D., Xing, B., Dimayuga, E., Saeed, F., Zhang, H., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066226 · Cited by 80
Specificity of Staphyloferrin B Recognition by the SirA Receptor from Staphylococcus aureus
Grigg, J. C., Cheung, J., Heinrichs, D. E., & Murphy, M. E. P. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.172924 · Cited by 71
Lrat-specific domain facilitates Vitamin A metabolism by domain swapping in HRASLS3
Golczak, M., Sears, A. E., Kiser, P. D., & Palczewski, K. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1687 · Cited by 58
Testosterone meets albumin – the molecular mechanism of sex hormone transport by serum albumins
Czub, M. P., Venkataramany, B. S., Majorek, K. A., Handing, K. B., Porebski, P. J., Beeram, S. R., Suh, K., Woolfork, A. G., Hage, D. S., Shabalin, I. G., et al. (2019) · Chemical Science · doi:10.1039/c8sc04397c · Cited by 61
Lingaraju, M., Johnsen, D., Schlundt, A., Langer, L. M., Basquin, J., Sattler, M., Heick Jensen, T., Falk, S., & Conti, E. (2019) · Nature Communications · doi:10.1038/s41467-019-11339-x · Cited by 55
Tsutsumi, N., Hwang, S., Waghray, D., Hansen, S., Jude, K. M., Wang, N., Miao, Y., Glassman, C. R., Caveney, N. A., Janda, C. Y., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2218238120 · Cited by 52
Structural basis of LRPPRC–SLIRP-dependent translation by the mitoribosome
Singh, V., Moran, J. C., Itoh, Y., Soto, I. C., Fontanesi, F., Couvillion, M., Huynen, M. A., Churchman, L. S., Barrientos, A., & Amunts, A. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01365-9 · Cited by 49
Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.
Vance, T. D. R., Olijve, L. L. C., Campbell, R. L., Voets, I. K., Davies, P. L., & Guo, S. (2014) · Bioscience Reports · doi:10.1042/bsr20140083 · Cited by 40
Zhai, Q., Landesman, M. B., Robinson, H., Sundquist, W. I., & Hill, C. P. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027466 · Cited by 31
McCullough, T. M., Choudhary, V., Akey, D. L., Skiba, M. A., Bernard, S. M., Kittendorf, J. D., Schmidt, J. J., Sherman, D. H., & Smith, J. L. (2024) · ACS Catalysis · doi:10.1021/acscatal.4c03637 · Cited by 8
Guo, Y., Shukla, S., Minasov, G., Inniss, N. L., Klose, T., Tokars, V. L., Mondragón, A., Otwinowski, Z., Borek, D., & Satchell, K. J. F. (2026) · Protein Science · doi:10.1002/pro.70609 · Cited by 1
Metadata
- Authors
- Painter, J., & Merritt, E. A.
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2006-03-18
- Volume
- 62
- Issue
- 4
- Pages
- 439-450
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2162244749
- Cited by
- 1,240
- References
- 0
- FWCI
- 42.75
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
