The Uppsala Electron-Density Server

Kleywegt, Gerard J.; Harris, Mark; Zou, Jin Yu; Taylor, Thomas C.; Wählby, Anders; Jones, T. Alwyn

doi:10.1107/s0907444904013253

Cited by 355 publications

(384 citation statements)

References 29 publications

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“…The electron density maps can be computed from structure factors deposited in the PDB (as in this study), downloaded from the Uppsala Electron Density Server, 38 or calculated in the course of crystallographic refinement. Ringer reads electron density maps in CCP4, X-PLOR, and CNS file formats.…”

Section: Ringermentioning

confidence: 99%

Automated electron‐density sampling reveals widespread conformational polymorphism in proteins

et al. 2010

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Although proteins populate large structural ensembles, X-ray diffraction data are traditionally interpreted using a single model. To search for evidence of alternate conformers, we developed a program, Ringer, which systematically samples electron density around the dihedral angles of protein side chains. In a diverse set of 402 structures, Ringer identified weak, nonrandom electron-density features that suggest of the presence of hidden, lowly populated conformations for >18% of uniquely modeled residues. Although these peaks occur at electron-density levels traditionally regarded as noise, statistically significant (P < 10 25 ) enrichment of peaks at successive rotameric v angles validates the assignment of these features as unmodeled conformations. Weak electron density corresponding to alternate rotamers also was detected in an accurate electron density map free of model bias. Ringer analysis of the high-resolution structures of free and peptide-bound calmodulin identified shifts in ensembles and connected the alternate conformations to ligand recognition. These results show that the signal in high-resolution electron density maps extends below the traditional 1 r cutoff, and crystalline proteins are more polymorphic than current crystallographic models. Ringer provides an objective, systematic method to identify previously undiscovered alternate conformations that can mediate protein folding and function.

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Section: Ringermentioning

confidence: 99%

Automated electron‐density sampling reveals widespread conformational polymorphism in proteins

et al. 2010

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“…† † Real-space correlation coefficient, F o map against F c map, as reported by REFMAC5. ‡ ‡ Returned by EDS validation server (Kleywegt et al, 2004) during deposition via autodep (EBI-MSD). § § Regions as defined in PROCHECK (Laskowski et al, 1993).…”

Section: Packing Analysis Of Trypsinmentioning

confidence: 99%

“…In a final polishing step, all Asn, Gln and His sidechain conformations were checked for chemical plausibility (Weichenberger & Sippl, 2006), and close distance deviations (bumps) of more than 0.2 Å from WHATCHECK targets were corrected (Hoft et al, 1996). Coordinates and structure factors (code 2j9n) have been deposited with the Protein Data Bank and validated during deposition at EBI-MSD via autodep and the EDS (Kleywegt et al, 2004) service.…”

Section: Structure Solution and Refinementmentioning

confidence: 99%

Operator-assisted harvesting of protein crystals using a universal micromanipulation robot

et al. 2007

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High-throughput crystallography has reached a level of automation where complete computer-assisted robotic crystallization pipelines are capable of cocktail preparation, crystallization plate setup, and inspection and interpretation of results. While mounting of crystal pins, data collection and structure solution are highly automated, crystal harvesting and cryocooling remain formidable challenges towards full automation. To address the final frontier in achieving fully automated high-throughput crystallography, the prototype of an anthropomorphic six-axis universal micromanipulation robot (UMR) has been designed and tested; this UMR is capable of operator-assisted harvesting and cryoquenching of protein crystals as small as 10 mm from a variety of 96-well plates. The UMR is equipped with a versatile tool exchanger providing full operational flexibility. Trypsin crystals harvested and cryoquenched using the UMR have yielded a 1.5 Å structure demonstrating the feasibility of robotic protein crystal harvesting.

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“…This structure was chosen based, in large part, on its high quality and its publication in Protein Science, a peer-reviewed journal, as opposed to being submitted directly to the PDB without an accompanying publication. Students were provided with a 2Fo-Fc electron density map downloaded from the EDS, which has served as the repository for data used to solve crystal structures in the PDB since 2004 [1]. The 2Fo-Fc map primarily depicts the electron density of the structure that has already been modeled.…”

Section: Assignmentmentioning

confidence: 99%

Undergraduates improve upon published crystal structure in class assignment

Horowitz

Koldewey

Bardwell

2014

Biochem Molecular Bio Educ

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Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the protein sequence. With minimal direction from the instructor on how the students should complete the assignment, the students fared remarkably well in this task, with over half the class able to reconstruct the original sequence with over 77% sequence identity, and with structures whose median ranked in the 91st percentile of all structures of comparable resolution in terms of structure quality. Fourteen percent of the students' structures produced Molprobity steric clash validation scores even better than that of the original structure, suggesting that multiple students achieved an improvement in the overall structure quality compared to the published structure. Students were able to delineate limiting case chemical environments, such as charged interactions or complete solvent exposure, but were less able to distinguish finer details of hydrogen bonding or hydrophobicity. Our results prompt several questions: why were students able to perform so well in their structural validation scores? How were some students able to outperform the 88% sequence identity mark that would constitute a perfect score, given the level of degenerate density or surface residues with poor density? And how can the methodology used by the best students inform the practices of professional X-ray crystallographers? V C 2014 by The International Union of Biochemistry and Molecular Biology, 42(5):398-404, 2014.Keywords: biophysical methods; protein structure function and folding; assessment and the design of probes for student understanding and learning; active learning; computational biology; laboratory exercises; learning and curriculum design; problem-based learning

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The Uppsala Electron-Density Server

Cited by 355 publications

References 29 publications

Automated electron‐density sampling reveals widespread conformational polymorphism in proteins

Automated electron‐density sampling reveals widespread conformational polymorphism in proteins

Operator-assisted harvesting of protein crystals using a universal micromanipulation robot

Undergraduates improve upon published crystal structure in class assignment

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