Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

Gye Won Han, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Krzysztof Ginalski, Marc-André Elsliger, Scott M. Brittain, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Tamara Astakhova, Herbert Axelrod, Jaume M. Canaves, Hsiu-Ju Chiu, Michael DiDonato, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema, Andreas Kreusch, Peter Kuhn, Mitchell D. Miller, Andrew T. Morse, Kin Moy, Edward Nigoghossian, Sylvia Oommachen, Jie Ouyang, Jessica Paulsen, Kevin Quijano, Ron Reyes, Chris Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, Jeff Velasquez, Xianhong Wang, Bill West, Aprilfawn White, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, and Ian A. Wilson* Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California University of California, San Diego, La Jolla, California Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland

[1]  Richard J Morris,et al.  Towards complete validated models in the next generation of ARP/wARP. , 2004, Acta crystallographica. Section D, Biological crystallography.

[2]  D. Downs,et al.  Lack of YggX Results in Chronic Oxidative Stress and Uncovers Subtle Defects in Fe-S Cluster Metabolism in Salmonella enterica , 2004, Journal of bacteriology.

[3]  Zukang Feng,et al.  Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. , 2004, Acta crystallographica. Section D, Biological crystallography.

[4]  Marcin von Grotthuss,et al.  Detecting distant homology with Meta-BASIC , 2004, Nucleic Acids Res..

[5]  David C. Richardson,et al.  MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes , 2004, Nucleic Acids Res..

[6]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

[7]  Jie Liang,et al.  CASTp: Computed Atlas of Surface Topography of proteins , 2003, Nucleic Acids Res..

[8]  Jimin Pei,et al.  PCMA: fast and accurate multiple sequence alignment based on profile consistency , 2003, Bioinform..

[9]  D. Downs,et al.  Lack of the ApbC or ApbE Protein Results in a Defect in Fe-S Cluster Metabolism in Salmonella enterica Serovar Typhimurium , 2003, Journal of bacteriology.

[10]  Martyn D Winn,et al.  Macromolecular TLS refinement in REFMAC at moderate resolutions. , 2003, Methods in enzymology.

[11]  Adam Godzik,et al.  Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Earl W. Cornell,et al.  An approach to rapid protein crystallization using nanodroplets , 2002 .

[13]  N. Colloc'h,et al.  Sequence and structural features of the T‐fold, an original tunnelling building unit , 2000, Proteins.

[14]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[15]  D. Downs,et al.  A Periplasmic Location Is Essential for the Role of the ApbE Lipoprotein in Thiamine Synthesis in Salmonella typhimurium , 1999, Journal of bacteriology.

[16]  Thomas C. Terwilliger,et al.  Automated MAD and MIR structure solution , 1999, Acta crystallographica. Section D, Biological crystallography.

[17]  S J Wodak,et al.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. , 1999, Acta crystallographica. Section D, Biological crystallography.

[18]  J. Thornton,et al.  PQS: a protein quaternary structure file server. , 1998, Trends in biochemical sciences.

[19]  David S. Moss,et al.  Error Estimates of Protein Structure Coordinates and Deviations from Standard Geometry by Full-Matrix Refinement of γB- and βB2-Crystallin , 1998 .

[20]  D. Downs,et al.  The apbE Gene Encodes a Lipoprotein Involved in Thiamine Synthesis in Salmonella typhimurium , 1998, Journal of bacteriology.

[21]  D S Moss,et al.  Error estimates of protein structure coordinates and deviations from standard geometry by full-matrix refinement of gammaB- and betaB2-crystallin. , 1998, Acta crystallographica. Section D, Biological crystallography.

[22]  T. Prangé,et al.  Crystal Structure of the protein drug urate oxidase-inhibitor complex at 2.05 Å resolution , 1997, Nature Structural Biology.

[23]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[24]  C. Sander,et al.  Dali: a network tool for protein structure comparison. , 1995, Trends in biochemical sciences.

[25]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[26]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[27]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[28]  B. Matthews.  Solvent content of protein crystals. , 1968, Journal of molecular biology.