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A quick solution: ab initio structure determination of a 19 kDa metalloproteinase using ACORN.

McAuley KE, Jia-Xing Y, Dodson EJ, Lehmbeck J, Østergaard PR, Wilson KS
Acta Crystallogr D Biol Crystallogr 57 1571-8 (2001)
Cited: 17 times
EuropePMC logo PMID: 11679721

Abstract

A data set from the metalloproteinase deuterolysin was collected at atomic resolution (1.0 A) with synchrotron radiation. The high resolution allowed the structure to be solved with the new direct-methods program ACORN using the coordinates of the Zn atom as a starting point. The phases obtained from ACORN were of sufficient quality to allow automated building to be carried out in ARP/wARP. Minimal manual rebuilding of the model was required and the structure determination was completed using the maximum-likelihood refinement program REFMAC. The whole process, starting from the processed and merged data and ending with a refined model, required less than 6 h of computational time.

Reviews - 1eb6 mentioned but not cited (1)

  1. Macromolecular ab initio phasing enforcing secondary and tertiary structure. Millán C, Sammito M, Usón I. IUCrJ 2 95-105 (2015)

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  1. Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures. Chen X, Weber I, Harrison RW. J Phys Chem B 112 12073-12080 (2008)
  2. On the Dielectric Boundary in Poisson-Boltzmann Calculations. Tjong H, Zhou HX. J Chem Theory Comput 4 507-514 (2008)
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  5. Antigen-binding properties of monoclonal antibodies reactive with EBNA1 and use in immunoaffinity chromatography. Duellman SJ, Burgess RR. PLoS ONE 4 e4614 (2009)
  6. Model validation: local diagnosis, correction and when to quit. Richardson JS, Williams CJ, Hintze BJ, Chen VB, Prisant MG, Videau LL, Richardson DC. Acta Crystallogr D Struct Biol 74 132-142 (2018)
  7. Reciprocal carbonyl-carbonyl interactions in small molecules and proteins. Rahim A, Saha P, Jha KK, Sukumar N, Sarma BK. Nat Commun 8 78 (2017)
  8. PAGAL - Properties and corresponding graphics of alpha helical structures in proteins. Chakraborty S, Rao B, Dandekar A. F1000Res 3 206 (2014)
  9. A new density-modification procedure extending the application of the recent |ρ|-based phasing algorithm to larger crystal structures. Rius J, Torrelles X. Acta Crystallogr A Found Adv 77 339-347 (2021)
  10. The oxygen-oxygen distance of water in crystallographic data sets. Palese LL. Data Brief 28 105076 (2020)


Reviews citing this publication (1)

  1. Structural aspects of the metzincin clan of metalloendopeptidases. Gomis-Rüth FX. Mol. Biotechnol. 24 157-202 (2003)

Articles citing this publication (5)

  1. Specific radiation damage can be used to solve macromolecular crystal structures. Ravelli RB, Leiros HK, Pan B, Caffrey M, McSweeney S. Structure 11 217-224 (2003)
  2. Molecular evolution of the deuterolysin (M35) family genes in Coccidioides. Li J, Yu L, Tian Y, Zhang KQ. PLoS ONE 7 e31536 (2012)
  3. New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics. Prisant MG, Williams CJ, Chen VB, Richardson JS, Richardson DC. Protein Sci 29 315-329 (2020)
  4. Letter Structural evidence of intramolecular propeptide inhibition of the aspzincin metalloendopeptidase AsaP1. Bogdanović X, Palm GJ, Schwenteit J, Singh RK, Gudmundsdóttir BK, Hinrichs W. FEBS Lett. 590 3280-3294 (2016)
  5. The M35 Metalloprotease Effector FocM35_1 Is Required for Full Virulence of Fusarium oxysporum f. sp. cubense Tropical Race 4. Zhang X, Huang H, Wu B, Xie J, Viljoen A, Wang W, Mostert D, Xie Y, Fu G, Xiang D, Lyu S, Liu S, Li C. Pathogens 10 670 (2021)


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