Validation of ligands in macromolecular structures determined by X-ray crystallography

Smart, Oliver S.; Horský, Vladimír; Gore, Swanand; Vařeková, Radka Svobodová; Bendová, Veronika; Kleywegt, Gerard J.; Velankar, Sameer

doi:10.1107/s2059798318002541

Cited by 56 publications

(45 citation statements)

References 52 publications

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“…Compared to the VIM‐1:ML302F complex, binding of hydrolysed meropenem to VIM‐2 is less well defined – in addition to the lower resolution, elevated B‐factors were observed for the hydrolysed meropenem ligand (overall B‐factor of 39.13 Å 2 compared to 16.99 Å 2 for the protein main chain). Nevertheless, refining the ligand at full occupancy yielded a real‐space correlation coefficient of 0.85 and real‐space R‐value of 0.25; parameters that indicate acceptable agreement of observed and calculated electron densities for bound ligand . This is confirmed by visual inspection; omit (| F o | − | F c | Φ calc ; Fig.…”

Section: Resultssupporting

confidence: 55%

“…13 A 2 compared to 16.99 A 2 for the protein main chain). Nevertheless, refining the ligand at full occupancy yielded a real-space correlation coefficient of 0.85 and real-space R-value of 0.25; parameters that indicate acceptable agreement of observed and calculated electron densities for bound ligand [37]. This is confirmed by visual inspection; omit (|F o | À |F c | Φ calc ; Fig.…”

Section: Interactions Of Vim-1 With Hydrolysed Meropenemsupporting

confidence: 58%

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Crystal structures of VIM‐1 complexes explain active site heterogeneity in VIM‐class metallo‐β‐lactamases

et al. 2018

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Metallo‐β‐Lactamases (MBLs) protect bacteria from almost all β‐lactam antibiotics. Verona integron‐encoded MBL (VIM) enzymes are among the most clinically important MBLs, with VIM‐1 increasing in carbapenem‐resistant Enterobacteriaceae ( Escherichia coli , Klebsiella pneumoniae ) that are among the hardest bacterial pathogens to treat. VIM enzymes display sequence variation at residues (224 and 228) that in related MBLs are conserved and participate in substrate binding. How they accommodate this variability, while retaining catalytic efficiency against a broad substrate range, has remained unclear. Here, we present crystal structures of VIM‐1 and its complexes with a substrate‐mimicking thioenolate inhibitor, ML302F, that restores meropenem activity against a range of VIM‐1 producing clinical strains, and the hydrolysed product of the carbapenem meropenem. Comparison of these two structures identifies a water‐mediated hydrogen bond, between the carboxylate group of substrate/inhibitor and the backbone carbonyl of the active site zinc ligand Cys221, that is common to both complexes. Structural comparisons show that the responsible Cys221‐bound water is observed in all known VIM structures, participates in carboxylate binding with other inhibitor classes, and thus effectively replicates the role of the conserved Lys224 in analogous complexes with other MBLs. These results provide a mechanism for substrate binding that permits the variation at positions 224 and 228 that is a hallmark of VIM MBLs. Enzymes EC 3.5.2.6 Databases Co‐ordinates and structure factors for protein structures described in this manuscript have been deposited in the Protein Data Bank ( www.rcsb.org/pdb ) with accession codes 5N5G (VIM‐1), 5N5H (VIM‐1:ML302F complex) and 5N5I (VIM‐1‐hydrolysed meropenem complex).

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Section: Resultssupporting

confidence: 55%

Section: Interactions Of Vim-1 With Hydrolysed Meropenemsupporting

confidence: 58%

Crystal structures of VIM‐1 complexes explain active site heterogeneity in VIM‐class metallo‐β‐lactamases

et al. 2018

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“…Quite common are issues with small-molecule ligands where mistakes may happen in determining their identity, placement, orientation and conformation. Since ligands by their nature are infinitely more varied than the standard amino acids and nucleotides, they are more difficult to build, refine and validate [37] [38] [39] [40] [41]. …”

Section: Validation Of Structural Data and Models Is (Still) Necessarymentioning

confidence: 99%

Structural biology data archiving – where we are and what lies ahead

2018

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For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank, Electron Microscopy Data Bank and Biological Magnetic Resonance Data Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilized to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists.

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“…In an accompanying publication (Smart et al, 2018) we specifically examine ligand validation and the relevant metrics, showing that further work is required to make the latter more reliable.…”

Section: Using Validation Informationmentioning

confidence: 99%

“…residues that show a poorer than expected fit to the electron density. This is followed by a table highlighting outliers for small-molecule ligands, which contains information about any issues with chirality when compared with the standard wwPDB Chemical Component Dictionary (CCD; Westbrook et al, 2015), outliers in geometry as highlighted using Mogul analysis, close contacts and issues with experimental evidence: electron density in the case of X-ray crystallographic structures, as assessed by local ligand density fit (LLDF) analysis (for a detailed examination of ligand validation, see Smart et al, 2018). The residue-level details concerning outliers are provided in section 3 of the VR, which contains a residue-level plot for each polymeric chain.…”

Section: Introductionmentioning

confidence: 99%

Worldwide Protein Data Bank validation information: usage and trends

Smart

Horský

Gore

et al. 2018

Acta Crystallogr D Struct Biol

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Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrends DB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

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Validation of ligands in macromolecular structures determined by X-ray crystallography

Cited by 56 publications

References 52 publications

Crystal structures of VIM‐1 complexes explain active site heterogeneity in VIM‐class metallo‐β‐lactamases

Crystal structures of VIM‐1 complexes explain active site heterogeneity in VIM‐class metallo‐β‐lactamases

Structural biology data archiving – where we are and what lies ahead

Worldwide Protein Data Bank validation information: usage and trends

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