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Volumn 12, Issue 2, 2011, Pages 83-95

SAD phasing using iodide ions in a high-throughput structural genomics environment

Author keywords

Experimental phasing; Iodide ions; SAD; Selenomethionine; Structural genomics; Structure determination

Indexed keywords

BACTERIAL ENZYME; BOL A LIKE PROTEIN; FRUCTOSE BISPHOSPHATE ALDOLASE; IODIDE ION; PHOSPHOSERINE PHOSPHATASE SERB; PROTOZOAL PROTEIN; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; IODIDE; PHOSPHATASE; PHOSPHOSERINE PHOSPHATASE;

EID: 80052613698     PISSN: 1345711X     EISSN: 15700267     Source Type: Journal    
DOI: 10.1007/s10969-011-9101-7     Document Type: Article
Times cited : (68)

References (60)
  • 2
    • 70350479575 scopus 로고    scopus 로고
    • The role of medical structural genomics in discovering new drugs for infectious diseases
    • Van Voorhis WC, Hol WG, Myler PJ, Stewart LJ (2009) The role of medical structural genomics in discovering new drugs for infectious diseases. PLoS Comput Biol 5:e1000530
    • (2009) PLoS Comput Biol , vol.5
    • Van Voorhis, W.C.1    Hol, W.G.2    Myler, P.J.3    Stewart, L.J.4
  • 3
    • 70349557379 scopus 로고    scopus 로고
    • Structural genomics and drug discovery for infectious diseases
    • Anderson WF (2009) Structural genomics and drug discovery for infectious diseases. Infect Disord Drug Targets 9:507-517
    • (2009) Infect Disord Drug Targets , vol.9 , pp. 507-517
    • Anderson, W.F.1
  • 4
    • 36549040856 scopus 로고    scopus 로고
    • Phase determination using halide ions
    • DOI 10.1385/1-59745-266-1:149, Macromolecular Crystallography Protocols, Volume 2: Structure Determination
    • Dauter M, Dauter Z (2007) Phase determination using halide ions. Methods Mol Biol 364:149-158 (Pubitemid 350185926)
    • (2007) Methods in Molecular Biology , vol.364 , pp. 149-158
    • Dauter, M.1    Dauter, Z.2
  • 6
    • 67349264483 scopus 로고    scopus 로고
    • The three-dimensional structure of the cytoplasmic domains of EpsF from the type 2 secretion system of Vibrio cholerae
    • Abendroth J, Mitchell DD, Korotkov KV, Johnson TL, Kreger A et al (2009) The three-dimensional structure of the cytoplasmic domains of EpsF from the type 2 secretion system of Vibrio cholerae. J Struct Biol 166:303-315
    • (2009) J Struct Biol , vol.166 , pp. 303-315
    • Abendroth, J.1    Mitchell, D.D.2    Korotkov, K.V.3    Johnson, T.L.4    Kreger, A.5
  • 7
    • 77958499676 scopus 로고    scopus 로고
    • Structure of a Burkholderia pseudomallei trimeric auto-transporter adhesin head
    • Edwards TE, Phan I, Abendroth J, Dieterich SH, Masoudi A et al (2010) Structure of a Burkholderia pseudomallei trimeric auto-transporter adhesin head. PLoS One 5:e12803
    • (2010) PLoS One , vol.5
    • Edwards, T.E.1    Phan, I.2    Abendroth, J.3    Dieterich, S.H.4    Masoudi, A.5
  • 8
    • 34447623057 scopus 로고    scopus 로고
    • SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kα X-ray source: Effects of data redundancy and completeness on structure solution
    • DOI 10.1107/S0907444907029174, PII S0907444907029174
    • Yogavel M, Gill J, Mishra PC, Sharma A (2007) SAD phasing of a structure based on cocrystallized iodides using an in-house Cu Kalpha X-ray source: effects of data redundancy and complete-ness on structure solution. Acta Crystallogr D Biol Crystallogr 63:931-934 (Pubitemid 47094576)
    • (2007) Acta Crystallographica Section D: Biological Crystallography , vol.63 , Issue.8 , pp. 931-934
    • Yogavel, M.1    Gill, J.2    Mishra, P.C.3    Sharma, A.4
  • 9
    • 66249136712 scopus 로고    scopus 로고
    • Iodide-SAD, SIR and SIRAS phasing for structure solution of a nucleosome assembly protein
    • Yogavel M, Gill J, Sharma A (2009) Iodide-SAD, SIR and SIRAS phasing for structure solution of a nucleosome assembly protein. Acta Crystallogr D Biol Crystallogr 65:618-622
    • (2009) Acta Crystallogr D Biol Crystallogr , vol.65 , pp. 618-622
    • Yogavel, M.1    Gill, J.2    Sharma, A.3
  • 10
    • 77952041888 scopus 로고    scopus 로고
    • Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: Structural polymorphism and HEPES-bound enzyme states
    • Yogavel M, Khan S, Bhatt TK, Sharma A (2010) Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states. Acta Crystallogr D Biol Crystallogr 66:584-592
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , pp. 584-592
    • Yogavel, M.1    Khan, S.2    Bhatt, T.K.3    Sharma, A.4
  • 11
    • 22544476228 scopus 로고    scopus 로고
    • The crystal structure of PfFabZ, the unique β-hydroxyacyl-ACP dehydratase involved in fatty acid biosynthesis of Plasmodium falciparum
    • DOI 10.1110/ps.051373005
    • Kostrewa D, Winkler FK, Folkers G, Scapozza L, Perozzo R (2005) The crystal structure of PfFabZ, the unique beta-hydrox-yacyl-ACP dehydratase involved in fatty acid biosynthesis of Plasmodiumfalciparum. Protein Sci 14:1570-1580 (Pubitemid 41014815)
    • (2005) Protein Science , vol.14 , Issue.6 , pp. 1570-1580
    • Kostrewa, D.1    Winkler, F.K.2    Folkers, G.3    Scapozza, L.4    Perozzo, R.5
  • 13
    • 77950860086 scopus 로고    scopus 로고
    • Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): Profound asymmetry in the crystal structure of the 'open' state
    • Buchko GW, Robinson H, Abendroth J, Staker BL, Myler PJ (2010) Structural characterization of Burkholderia pseudomallei adenylate kinase (Adk): profound asymmetry in the crystal structure of the 'open' state. Biochem Biophys Res Commun 394:1012-1017
    • (2010) Biochem Biophys Res Commun , vol.394 , pp. 1012-1017
    • Buchko, G.W.1    Robinson, H.2    Abendroth, J.3    Staker, B.L.4    Myler, P.J.5
  • 14
    • 77958149212 scopus 로고    scopus 로고
    • Biological and structural characterization of a host-adapting amino acid in influenza virus
    • Yamada S, Hatta M, Staker BL, Watanabe S, Imai M et al (2010) Biological and structural characterization of a host-adapting amino acid in influenza virus. PLoS Pathog 6:e1001034
    • (2010) PLoS Pathog , vol.6
    • Yamada, S.1    Hatta, M.2    Staker, B.L.3    Watanabe, S.4    Imai, M.5
  • 15
    • 0025085655 scopus 로고
    • Ligation-independent cloning of PCR products (LIC-PCR
    • Aslanidis C, de Jong PJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18:6069-6074
    • (1990) Nucleic Acids Res , vol.18 , pp. 6069-6074
    • Aslanidis, C.1    De Jong, P.J.2
  • 16
    • 65649112893 scopus 로고    scopus 로고
    • Gene composer: Database software for protein construct design, codon engineering, and gene synthesis
    • Lorimer D, Raymond A, Walchli J, Mixon M, Barrow A et al (2009) Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol 9:36
    • (2009) BMC Biotechnol , vol.9 , pp. 36
    • Lorimer, D.1    Raymond, A.2    Walchli, J.3    Mixon, M.4    Barrow, A.5
  • 17
    • 65649096202 scopus 로고    scopus 로고
    • Combined protein construct and synthetic gene engi-neering for heterologous protein expression and crystallization using gene composer
    • Raymond A, Lovell S, Lorimer D, Walchli J, Mixon M et al (2009) Combined protein construct and synthetic gene engi-neering for heterologous protein expression and crystallization using gene composer. BMC Biotechnol 9:37
    • (2009) BMC Biotechnol , vol.9 , pp. 37
    • Raymond, A.1    Lovell, S.2    Lorimer, D.3    Walchli, J.4    Mixon, M.5
  • 18
    • 14844294424 scopus 로고    scopus 로고
    • Protein production by auto-induction in high density shaking cultures
    • Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif41:207-234
    • (2005) Protein Expr Purif , vol.41 , pp. 207-234
    • Studier, F.W.1
  • 21
    • 77957337491 scopus 로고    scopus 로고
    • Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system
    • Gerdts CJ, Stahl GL, Napuli A, Staker B, Abendroth J et al (2010) Nanovolume optimization of protein crystal growth using the microcapillary protein crystallization system. J Appl Crsyt 43:1078
    • (2010) J Appl Crsyt , vol.43 , pp. 1078
    • Gerdts, C.J.1    Stahl, G.L.2    Napuli, A.3    Staker, B.4    Abendroth, J.5
  • 22
    • 64549153594 scopus 로고    scopus 로고
    • In situ proteolysis to generate crystals for structure determination: An update
    • Wernimont A, Edwards A (2009) In situ proteolysis to generate crystals for structure determination: an update. PLoS One 4:e5094
    • (2009) PLoS One , vol.4
    • Wernimont, A.1    Edwards, A.2
  • 23
    • 42449125742 scopus 로고    scopus 로고
    • Improved success of sparse matrix protein crystallization screening with heterogeneous nucleating agents
    • Thakur AS, Robin G, Guncar G, Saunders NF, Newman J et al (2007) Improved success of sparse matrix protein crystallization screening with heterogeneous nucleating agents. PLoS One 2:e1091
    • (2007) PLoS One , vol.2
    • Thakur, A.S.1    Robin, G.2    Guncar, G.3    Saunders, N.F.4    Newman, J.5
  • 26
    • 37549039510 scopus 로고    scopus 로고
    • A short history of SHELX
    • Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112-122
    • (2008) Acta Crystallogr A , vol.64 , pp. 112-122
    • Sheldrick, G.M.1
  • 28
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project Number 4
    • Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760-763
    • (1994) Acta Crystallogr D Biol Crystallogr , vol.50 , pp. 760-763
  • 29
    • 77950798648 scopus 로고    scopus 로고
    • Recent developments in classical density modification
    • Cowtan K (2010) Recent developments in classical density modification. Acta Crystallogr D Biol Crystallogr 66:470-478
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , pp. 470-478
    • Cowtan, K.1
  • 30
    • 33748337934 scopus 로고    scopus 로고
    • The Buccaneer software for automated model building. 1. Tracing protein chains
    • DOI 10.1107/S0907444906022116
    • Cowtan K (2006) The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr 62:1002-1011 (Pubitemid 44337374)
    • (2006) Acta Crystallographica Section D: Biological Crystallography , vol.62 , Issue.9 , pp. 1002-1011
    • Cowtan, K.1
  • 31
    • 50249136103 scopus 로고    scopus 로고
    • Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7
    • Langer G, Cohen SX, Lamzin VS, Perrakis A (2008) Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat Protoc 3:1171-1179
    • (2008) Nat Protoc , vol.3 , pp. 1171-1179
    • Langer, G.1    Cohen, S.X.2    Lamzin, V.S.3    Perrakis, A.4
  • 34
    • 34547592557 scopus 로고    scopus 로고
    • MolProbity: All-atom contacts and structure validation for proteins and nucleic acids
    • Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ et al (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35:W375-W383
    • (2007) Nucleic Acids Res , vol.35
    • Davis, I.W.1    Leaver-Fay, A.2    Chen, V.B.3    Block, J.N.4    Kapral, G.J.5
  • 36
    • 56649108117 scopus 로고    scopus 로고
    • The interdependence of wavelength, redundancy and dose in sulfur SAD experiments
    • Cianci M, Helliwell JR, Suzuki A (2008) The interdependence of wavelength, redundancy and dose in sulfur SAD experiments. Acta Crystallogr D Biol Crystallogr 64:1196-1209
    • (2008) Acta Crystallogr D Biol Crystallogr , vol.64 , pp. 1196-1209
    • Cianci, M.1    Helliwell, J.R.2    Suzuki, A.3
  • 39
    • 0014432781 scopus 로고
    • Solvent content of protein crystals
    • Matthews BW (1968) Solvent content of protein crystals. J Mol Biol 33:491-497
    • (1968) J Mol Biol , vol.33 , pp. 491-497
    • Matthews, B.W.1
  • 40
    • 48349090695 scopus 로고    scopus 로고
    • Babesiosis: Recent insights into an ancient disease
    • Hunfeld KP, Hildebrandt A, Gray JS (2008) Babesiosis: recent insights into an ancient disease. Int J Parasitol 38:1219-1237
    • (2008) Int J Parasitol , vol.38 , pp. 1219-1237
    • Hunfeld, K.P.1    Hildebrandt, A.2    Gray, J.S.3
  • 41
    • 0033009562 scopus 로고    scopus 로고
    • The stationary-phase morphogene bolA from Escherichia coli is induced by stress during early stages of growth
    • DOI 10.1046/j.1365-2958.1999.01397.x
    • Santos JM, Freire P, Vicente M, Arraiano CM (1999) The sta-tionary-phase morphogene bolA from Escherichia coli is induced by stress during early stages of growth. Mol Microbiol 32: 789-798 (Pubitemid 29241519)
    • (1999) Molecular Microbiology , vol.32 , Issue.4 , pp. 789-798
    • Santos, J.M.1    Freire, P.2    Vicente, M.3    Arraiano, C.M.4
  • 43
    • 33947191879 scopus 로고    scopus 로고
    • An engineered second disulfide bond restricts lymphotactin/XCL1 to a chemokine-like conformation with XCR1 agonist activity
    • DOI 10.1021/bi602365d
    • Tuinstra RL, Peterson FC, Elgin ES, Pelzek AJ, Volkman BF (2007) An engineered second disulfide bond restricts lymphot-actin/XCL1 to a chemokine-like conformation with XCR1 ago-nist activity. Biochemistry 46:2564-2573 (Pubitemid 46417900)
    • (2007) Biochemistry , vol.46 , Issue.10 , pp. 2564-2573
    • Tuinstra, R.L.1    Peterson, F.C.2    Elgin, E.S.3    Pelzek, A.J.4    Volkman, B.F.5
  • 44
    • 0034436062 scopus 로고    scopus 로고
    • Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures
    • DOI 10.1016/S0969-2126(00)00524-4, PII S0969212600005244
    • Chen YW, Dodson EJ, Kleywegt GJ (2000) Does NMR mean ''not for molecular replacement''? Using NMR-based search models to solve protein crystal structures. Structure 8:R213-R220 (Pubitemid 32667475)
    • (2000) Structure , vol.8 , Issue.11
    • Yu Wai Chen1    Dodson, E.J.2    Kleywegt, G.J.3
  • 45
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • DOI 10.1107/S0907444904026460
    • Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60:2256-2268 (Pubitemid 41742778)
    • (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.12 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 46
    • 15744382301 scopus 로고    scopus 로고
    • Coccidioidomycosis\-a fungal disease of the Americas
    • Hector RF, Laniado-Laborin R (2005) Coccidioidomycosis\-a fungal disease of the Americas. PLoS Med 2:e2
    • (2005) PLoS Med , vol.2
    • Hector, R.F.1    Laniado-Laborin, R.2
  • 47
    • 70349645483 scopus 로고    scopus 로고
    • Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
    • Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR et al (2009) Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res 19: 1722-1731
    • (2009) Genome Res , vol.19 , pp. 1722-1731
    • Sharpton, T.J.1    Stajich, J.E.2    Rounsley, S.D.3    Gardner, M.J.4    Wortman, J.R.5
  • 50
    • 77950821956 scopus 로고    scopus 로고
    • Selenium incorporation using recombinant techniques
    • Walden H (2010) Selenium incorporation using recombinant techniques. Acta Crystallogr D Biol Crystallogr 66:352-357
    • (2010) Acta Crystallogr D Biol Crystallogr , vol.66 , pp. 352-357
    • Walden, H.1
  • 51
    • 80052613464 scopus 로고    scopus 로고
    • Recent major improvements to the ALS sector 5 macromolecular crystallography beamlines
    • Morton S, Glossinger J, Smith-Baumann A, McKean JP, Trame C et al (2007) Recent major improvements to the ALS sector 5 macromolecular crystallography beamlines. Sync Rad News 20:23-30
    • (2007) Sync Rad News , vol.20 , pp. 23-30
    • Morton, S.1    Glossinger, J.2    Smith-Baumann, A.3    McKean, J.P.4    Trame, C.5
  • 52
    • 0033392524 scopus 로고    scopus 로고
    • Exploring structure space: A protein structure initiative
    • Terwilliger TC, Berendzen J (1999) Exploring structure space. A protein structure initiative. Genetica 106:141-147 (Pubitemid 30049242)
    • (1999) Genetica , vol.106 , Issue.1-2 , pp. 141-147
    • Terwilliger, T.C.1    Berendzen, J.2
  • 53
    • 3543110895 scopus 로고    scopus 로고
    • Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination
    • DOI 10.1023/B:JSFG.0000029196.87615.6e
    • Stols L, Millard CS, DementievaI, Donnelly MI (2004) Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination. J Struct Funct Genomics 5:95-102 (Pubitemid 39030625)
    • (2004) Journal of Structural and Functional Genomics , vol.5 , Issue.1-2 , pp. 95-102
    • Stols, L.1    Millard, C.S.2    Dementieva, I.3    Donnelly, M.I.4
  • 55
    • 0037317546 scopus 로고    scopus 로고
    • Specific radiation damage can be used to solve macromolecular crystal structures
    • DOI 10.1016/S0969-2126(03)00006-6, PII S0969212603000066
    • Ravelli RB, Leiros HK, Pan B, Caffrey M, McSweeney S (2003) Specific radiation damage can be used to solve macromolecular crystal structures. Structure 11:217-224 (Pubitemid 36183645)
    • (2003) Structure , vol.11 , Issue.2 , pp. 217-224
    • Ravelli, R.B.G.1    Leiros, H.-K.S.2    Pan, B.3    Caffrey, M.4    McSweeney, S.5
  • 56
    • 33646559851 scopus 로고    scopus 로고
    • New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)
    • DOI 10.1107/S0907444905041909
    • Miyatake H, Hasegawa T, Yamano A (2006) New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL). Acta Crystallogr D Biol Crystallogr 62:280-289 (Pubitemid 44185137)
    • (2006) Acta Crystallographica Section D: Biological Crystallography , vol.62 , Issue.3 , pp. 280-289
    • Miyatake, H.1    Hasegawa, T.2    Yamano, A.3
  • 59
    • 0000771276 scopus 로고
    • A suite ofprograms for calculating x-ray absorption, reflection and diffraction performance for a variety of materials at arbitrary wavelengths
    • Brennan S, Cowan PL (1992) A suite ofprograms for calculating x-ray absorption, reflection and diffraction performance for a variety of materials at arbitrary wavelengths. Rev Sci Instrum 63:850
    • (1992) Rev Sci Instrum , vol.63 , pp. 850
    • Brennan, S.1    Cowan, P.L.2
  • 60
    • 79151473963 scopus 로고    scopus 로고
    • Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c
    • Buchko GW, Phan I, Myler PJ, Terwilliger TC, Kim YC (2011) Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c. Arch Biochem Biophys 506(2):150-156
    • (2011) Arch Biochem Biophys , vol.506 , Issue.2 , pp. 150-156
    • Buchko, G.W.1    Phan, I.2    Myler, P.J.3    Terwilliger, T.C.4    Kim, Y.C.5


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