Crystal structure of the YgfY from Escherichia coli, a protein that may be involved in transcriptional regulation

Proteins: Structure, Function and Genetics

Volumn 58, Issue 3, 2005, Pages 759-763

  Lim, Kap ^a   Doseeva, Victoria ^a   Demirkan, Elif Sarikaya ^a   Pullalarevu, Sadhana ^a   Krajewski, Wojciech ^a   Galkin, Andrey ^a   Howard, Andrew ^b   Herzberg, Osnat ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b Illinois Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN YGFY; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; CRYSTALLIZATION; ESCHERICHIA COLI; HYDROPHOBICITY; LIGHT SCATTERING; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN INTERACTION; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; STEREOISOMERISM; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 12944281621     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20337     Document Type: Article

References (22)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25: 3389-3402.
2. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004;304:66-74.
3. Enyenihi AH, Saunders WS. Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 2003;163:47-54.
4. Liu G, Sukumaran DK, Xu D, Chiang Y, Acton T, Goldsmith-Fischman S, Honig B, Montelione GT, Szyperski T. NMR structure of the hypothetical protein NMA1147 from Neisseria meningitidis reveals a distinct 5-helix bundle. Proteins 2004;55:756-758.
5. Otwinowski Z, Minor W. Processing of x-ray diffraction data collected in oscillation mode. Meth Enzymol 1997;276:307-326.
6. Schneider TR, Sheldrick GM. Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr 2002;58:1772-1779.
7. Uson I, Sheldrick GM. Advances in direct methods for protein crystallography. Curr Opin Struct Biol 1999;9:643-648.
8. Otwinowski Z. Maximum likelihood refinement of heavy atom parameters. Paper presented at the Isomorphous replacement and anomalous scattering, Warrington, UK; 1991.
9. CCP4. The CCP4 suite: programs for protein crystallography. Acta Crystallgr D Biol Crystallogr 1994;50:760-763.
10. Terwilliger TC. Maximum-likelihood density modification using pattern recognition of structural motifs. Acta Crystallogr D Biol Crystallogr 2001;57:1755-1762.
11. Jones TA, Zou JY, Cowan SW, Kjeldgaard. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 1991:47;110-119.
12. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
13. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood methods. Acta Crystallog 1997;D53:240-255.
14. Read RJ. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D Biol Crystallogr 2001;57: 1373-1382.
15. Laskowski RA, MacArthur MW, Moss DS, Thornton J. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
16. Kraullis PJ. A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24:946-950.
17. Bacon DJ, Anderson WF. A fast algorithm for rendering space-filling molecule pictures. J Mol Graph 1988;6:219-220.
18. Merritt EA, Bacon DJ. Raster3D: Photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
19. Stahlberg J, Divne C, Koivula A, Piens K, Claeyssens M, Teeri TT, Jones TA. Activity studies and crystal structures of catalytically deficient mutants of cellobiohydrolase I from Trichoderma reesei. J Mol Biol 1996;264:337-349.
20. Shoham M, Yonath A, Sussman JL, Moult J, Traub W, Kalb AJ. Crystal structure of demetallized concanavalin A: the metal-binding region. J Mol Biol 1979;131:137-155.
21. Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;247:536-540.
22. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002;30:264-267.