Structures Solved ab initio by SnB

Full Structures (>250 Atoms)

1. Vancomycin (tetragonal)
   • PDB ID No:
   • Chem.Formula: 2 (C66 H75 CL2 N9 O24 . HCl) . 51 (H20)
   • SnB Solution: loll@pharm.med.upenn.edu (Patrick Loll)
   • Citation: Loll, P.J., Bevivino, A.E., Korty, B.D. & Axelsen, P.H. (1977). Simultaneous recognition of a carboxylate-containing ligand and intermolecular surrogate ligand in the crystal structure of an asymmetric vancomycin dimer, J. Am. Chem. Soc. 119, 1516-1522.
     
     
2. Dimerization Domain of HNF-1a
   • PDB ID No:
• Chem.Formula: (C161 H234 N39 O49) . 31 (H2O)
• SnB Solution: narayana@biochemistry.cwru.edu (Narendra Narayana)
• Citation:
  
  
3. Conotoxin EpI
   • PDB ID No:
• Chem.Formula:
• SnB Solution:
• Citation: Hu, S.-H., Loughnan, M., Miller, R., Weeks, C.M., Blessing,  R.H., Alewood, P.F., Lewis, R.J. & Martin, J.L. (1998). The 1.1Å resolution crystal structure of [Tyr¹⁵]-EpI, a novel a-conotoxin from Conus episcopatus, solved by direct methods. Biochemistry 37, 11425-11433.
  
  
4. Macrolide
   • Chem.Formula: 8 (C28 N3 O6)
   • SnB Solution: soyer@lmcp.jussieu.fr (Alain Soyer)
   • Citation: Bachet, B. & Soyer, A. (1998). Premiere experience avec Shake-and-Bake, Colloque de l'Association Francaise de Cristallographie, Orleans, 24-27 Fevrier.
     
     
5. Gramicidin A
• PDB ID No: 1GMA
• Chem.Formula: 2 (C99 H140 N20 O17) . 15 (C2H5OH)
• SnB Solution: miller@hwi.buffalo.edu (Russ Miller)
• Citation(original structure determination): Langs, D.A. (1998). Three-dimensional structure at 0.86A of the uncomplexed form of the transmembrane ion channel peptide Gramicidin A, Science 241, 188-191.
  
  
6. DMSO d6 Peptide
   • Chem.Formula: 8 (C29 H37 N5 O6) . 6 (H2O)
   • SnB Solution: simardmi@ere.umontreal.ca (Michel Simard)
   • Citation: ASC meeting 1998, Boston, Poster 295
     
     
7. Er-1 Pheromone
   • PDB ID No: 2ERL
   • Chem.Formula: (C183 H276 N46 O67 S7) . C2H5OH . 22 (H20)
   • SnB Solution: dha@ewald.mbi.ucla.edu (Dan Anderson)
   • Citation: Anderson, D.H., Weiss, M.S. & Eisenberg, D. (1996). A challenging case for protein crystal structure determination: the mating pheromone Er-1 from Euplotes raikovi, Acta Cryst. D52, 469-480.
     
     
8. Vancomycin Aglycon
   • PDB ID No:
   • Chem.Formula:
   • SnB Solution: loll@pharm.med.upenn.edu (Patrick Loll)
   • Citation:
     
     
9. Crambin
   • PDB ID No: 1CNR
   • Chem.Formula: (C202 H321 N55 O64 S6) . ~75 (H2O)
   • SnB Solution: miller@hwi.buffalo.edu (Russ Miller)
   • Citation: Weeks, C.M., Hauptman, H.A., Smith, G.D., Blessing, R.H., Teeter, M.M. & Miller, R. (1995). Crambin: a direct solution for a 400 atom structure, Acta Cryst. D51, 33-38.
     
     
10. A-DNA Decamer Duplex
    • Chem.Formula:
    • SnB Solution:
    • Citation: Egli, M., Tereshko, V., Teplova, M., Minasov, G., Joachimiak, A., Sanishvili, R., Weeks, C.M., Miller, R., Maier, M.A., An, H., Cook, P.D. & Manoharan, M. (2000). X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution. Biopolymers (Nucleic Acid Sciences) 48, 234-252.
      
      
11. Alpha-1 Peptide
    • PDB ID No:
    • Chem.Formula: C290 H530 N62 O118 Cl1 (includes solvent)
    • SnB Solution: prive@oci.utoronto.ca (Gil Prive)
    • Citation: Prive, G., Anderson, D.H., Wesson, L., Cascio, D. & Eisenberg, D. (1999). Packed protein bilayers in the 0.9Å resolution structure of a designed alpha helical bundle, Protein Science 8, 1400-1409.
      
      
12. Rubredoxin
    • PDB ID No: 8RXN
    • Chem.Formula: (C245 H360 N58 O181 S5) . Fe . SO4 . 102 (H2O)
    • SnB Solution: miller@hwi.buffalo.edu (Russ Miller)
    • Citation (original structure determination): Z. Dauter, L.C. Sieker, and K.S. Wilson, "Refinement of Rubredoxin from Desulfovibrio vulgaris at 1.0A with and without restraints," Acta Cryst. B48, 42-59, 1992.
      
      
13. Vancomycin (trigonal)
    • PDB ID No:
    • Chem.Formula: 4 (C71 H84 N10 O27 Cl2) . 4 (HCl)
    • SnB Solution: miller@cs.buffalo.edu (Russ Miller)
    • Citation: Loll, P.J., Miller, R., Weeks, C.M. & Axelsen, P.H. (1998). A ligand-mediated dimerization mode for vancomycin, Chemistry and Biology 5, 293-298.
      
      
14. Bucandin
    • PDB ID No:
    • Chem.Formula: C293 N82 O94 S11 . 118 (H2O)
    • Data Owner: pkuhn@stanford.edu (Peter Kuhn)
    • SnB Solution: ash@smb.slac.stanford.edu (Ashley Deacon)
    • Citation: Kuhn, P., Deacon, A.M., Comoso, S., Rajaseger, G., Kini, R.M., Uson, I. & Kolatkar, P.R.
      
      
15. RNA/DNA Hybrid Decamer caaagaaaag / CTTTTCTTTG
    • Chem.Formula:
    • SnB Solution: gyewon@mbi.ucla.edu (Gye Won Han)
    • Citation:
      
      
16. Scorpion Toxin II
    • PDB ID No: 1PTX (1.3A)
    • Chem.Formula: C313 H464 N88 O96 S8 . 119 (H20)
    • SnB Solution: miller@hwi.buffalo.edu (Russ Miller)
    • Citation: Smith, G.D., Blessing, R.H., Ealick, S.E., Fontecilla-Camps, J.C., Hauptman, H.A., Housset, D., Langs, D.A. & Miller, R. (1997). The ab initio structure and refinement of a scorpion protein toxin, Acta Cryst. D53, 551-557.
      
      
17. HEW Lysozyme
    • PDB ID No: 1LZT (1.5A resolution)
    • Chem.Formula: C600,O400,N200,S10
    • SnB Solution: ash@smb.slac.stanford.edu (Ashley Deacon)
    • Citation: Deacon, A.M., Weeks, C.M., Miller, R. & Ealick, S.E. (1998). The Shake-and-Bake structure determination of triclinic lysozyme, Proc. Natl. Acad. Sci. USA, 95, 9284-9289.
      
      
18. Calmodulin
    • PDB ID No:
    • Chem.Formula: C720 N200 O250 S8 Ca5
    • Data Owner: wilson@laplace.csb.yale.edu (Mark Wilson)
    • SnB Solution: ash@smb.slac.stanford.edu (Ashley Deacon)
    • Citation:

Substructures (>20 Se)

1. Hepatitis C Virus NS5B RNA-Dependent RNA Polymerase
   • PDB ID No:
   • Citation: Lesburg, C.A., Cable, M.B., Ferrari, E., Hong, Z., Mannarino, A.F. & Weber, P.C. (1999). Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nature Structural Biology 6, 937-934.
     
     
2. Human S-Adenosylmethionine Decarboxylase
   • PDB ID No:
   • Citation: Ekstrom, J.L., Mathews, I.I., Stanley, B.A., Pegg, A.E. & Ealick, S.E. (1999). The crystal structure of human S-adenosylmethionine decarboxylase at 2.25Å resolution reveals a novel fold. Structure 7, 583-595.
     
     
3. Orotidine 5’-Monophosphate Decarboxylase
   • PDB ID No:
   • Citation: Appleby, T.C., Kinsland, C., Begley, T.P. & Ealick, S.E. (2000). The crystal structure and mechanism of orotidine 5’-monophosphate decarboxylase. Proc. Natl. Acad. Sci. USA, 97, 2005-2010.
     
     
4. Aminoimidazole Ribonucleotide Synthetase (PurM)
   • PDB ID No:
   • Citation: Li, C., Kappock, T.J., Stubbe, J., Weaver, T.M. & Ealick, S.E. (1999). X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5Å resolution. Structure 7, 1155-1166.
     
     
5. S-Adenosylhomocysteine Hydrolase
   • PDB ID No:
   • Citation: Turner, M.A., Yuan, C.-S., Borchardt, R.T., Hershfield, M.S., Smith, G.D. & Howell, P.L. (1998). Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. Nature Structural Biology 5, 369-375.
     
     
6. Enzyme 1 from the Pyruvate Dehydrogenase Multi-enzyme Complex
   • PDB ID No:
   • SnB Solution: fureyw@pitt.edu (Bill Furey)
   • Citation:
     
     
7. Human EphB2 Receptor SAM Domain
   • PDB ID No:
   • Citation: Thanos, C.D., Goodwill, K.E. & Bowie, J.U. (1999). Oligomeric structure of the human EphB2 receptor SAM domain. Science 283, 833-836.
     
     
8. Arylamine N-Acetyltransferase from Salmonella typhimurium
   • PDB ID No:
   • SnB Solution: martin@biop.ox.ac.uk (Martin Noble)
   • Citation: Sinclair, J.C. et. al. (2000). The crystal structure of arylamine N-acetyltransferase reveals a catalytic triad. Nature Structural Biology, in press.
     
     
9. MutS Mismatch Repair Protein from E. coli
   • PDB ID No:
   • SnB Solution: perrakis@embl-grenoble.fr (Anastassis Perrakis)
   • Citation:
     
     
10. Nicotinamide Nucleotide Transhydrogenase (domain I from R. rubrum)
    • PDB ID No:
    • SnB Solution: dave@scripps.edu (Dave Stout)
    • Citation:
      
      
11. Human HMG-CoA Reductase
    • PDB ID No:
    • SnB Solution: eva@chop.swmed.edu (Eva Istvan)
    • Citation: Istvan, E.S., Palnitkar, M., Buchanan, S.K. & Deisenhofer, J. (2000). Crystal structure of the catalytic portion of human HMG-CoA reductase: insights into regulation of activity and catalysis. EMBO J. 19, 819-830.
      
      
12. ADP-L-Glycero-D-Mannoheptose 6-Epimerase
    • PDB ID No:
    • SnB Solution: ash@smb.slac.stanford.edu (Ashley Deacon)
    • Citation: Deacon, A.M., Ni, Y.S., Coleman, W.G. Jr. & Ealick, S.E. (2000).  The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist. Structure 8, 453-462.
      
      
13. Neurospora crassa 3-Carboxy-cis,cis-muconate Lactonizing Enzyme
    • PDB ID No:
    • SnB Solution: tommi.kajander@helsinki.fi (Tommi Kajander)
    • Citation:
      
      
14. Ketopantoate Hydroxymethyltransferase from E. coli
    • PDB ID No:
    • SnB Solution: loretta@scripps.edu (Frank von Delft)
    • Citation: