Automated MAD and MIR structure solution

Terwilliger, Thomas C.; Berendzen, Joel

doi:10.1107/s0907444999000839

Cited by 3,076 publications

(1,469 citation statements)

References 29 publications

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“…Selenium sites were determined, and the initial phases were calculated with use of the SAD method using SOLVE. 9 After improving phases, approximately 50% of the overall structure of PH1602-extein was automatically built by RESOLVE. 10 The remaining 50% of the protein was traced manually over the initial map using O.…”

Section: Materials and Methods Cloning Of The Gene Encoding Ph1602-ementioning

confidence: 99%

Crystal structure of an RtcB homolog protein (PH1602‐extein protein) from Pyrococcus horikoshii reveals a novel fold

et al. 2006

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Section: Materials and Methods Cloning Of The Gene Encoding Ph1602-ementioning

confidence: 99%

Crystal structure of an RtcB homolog protein (PH1602‐extein protein) from Pyrococcus horikoshii reveals a novel fold

et al. 2006

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“…27 The phases were further improved by refinement of heavy atoms in SOLVE. 28 After density modification, 65% of the residues were automatically built by RESOLVE. 16 The model was completed using COOT.…”

Section: Protein Crystallizationmentioning

confidence: 99%

Atomic resolution structure of the cytoplasmic domain of Yersinia pestis YscU, a regulatory switch involved in type III secretion

et al. 2009

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Crystal structures of cleaved and uncleaved forms of the YscU cytoplasmic domain, an essential component of the type III secretion system (T3SS) in Yersinia pestis, have been solved by single-wavelength anomolous dispersion and refined with X-ray diffraction data extending up to atomic resolution (1.13 Å ). These crystallographic studies provide structural insights into the conformational changes induced upon auto-cleavage of the cytoplasmic domain of YscU. The structures indicate that the cleaved fragments remain bound to each other. The conserved NPTH sequence that contains the site of the N263-P264 peptide bond cleavage is found on a b-turn which, upon cleavage, undergoes a major reorientation of the loop away from the catalytic N263, resulting in altered electrostatic surface features at the site of cleavage. Additionally, a significant conformational change was observed in the N-terminal linker regions of the cleaved and noncleaved forms of YscU which may correspond to the molecular switch that influences substrate specificity. The YscU structures determined here also are in good agreement with the auto-cleavage mechanism described for the flagellar homolog FlhB and E. coli EscU.

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“…Data were collected at beamline X9A of the National Synchrotron Light Source (NSLS), and processed and merged with the HKL program suite. 13 Se positions were located with SOLVE, 14 and the first model was built with Resolve. 15 Waters were added with Arp_waters (ARP/ wARP version 5.0), 16 and refinement was performed with Refmac 5.0 17 from the CCP4 program suite.…”

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confidence: 99%