Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris

Buß M, Geerds C, Patschkowski T, Niehaus K, Niemann H (2018)
Acta Crystallographica Section F Structural Biology Communications 74(6): 345-350.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Buß, MarenUniBi; Geerds, ChristinaUniBi; Patschkowski, ThomasUniBi; Niehaus, KarstenUniBi; Niemann, HartmutUniBi
Einrichtung
Fakultät für Chemie > Biochemie IV
Fakultät für Biologie > Proteom- und Metabolomforschung
Erscheinungsjahr
2018
Zeitschriftentitel
Acta Crystallographica Section F Structural Biology Communications
Band
74
Ausgabe
6
Seite(n)
345-350
ISSN
2053-230X
Page URI
https://pub.uni-bielefeld.de/record/2920494

Zitieren

Buß M, Geerds C, Patschkowski T, Niehaus K, Niemann H. Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallographica Section F Structural Biology Communications. 2018;74(6):345-350.
Buß, M., Geerds, C., Patschkowski, T., Niehaus, K., & Niemann, H. (2018). Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallographica Section F Structural Biology Communications, 74(6), 345-350. doi:10.1107/s2053230x18006933
Buß, Maren, Geerds, Christina, Patschkowski, Thomas, Niehaus, Karsten, and Niemann, Hartmut. 2018. “Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris”. Acta Crystallographica Section F Structural Biology Communications 74 (6): 345-350.
Buß, M., Geerds, C., Patschkowski, T., Niehaus, K., and Niemann, H. (2018). Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallographica Section F Structural Biology Communications 74, 345-350.
Buß, M., et al., 2018. Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallographica Section F Structural Biology Communications, 74(6), p 345-350.
M. Buß, et al., “Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris”, Acta Crystallographica Section F Structural Biology Communications, vol. 74, 2018, pp. 345-350.
Buß, M., Geerds, C., Patschkowski, T., Niehaus, K., Niemann, H.: Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallographica Section F Structural Biology Communications. 74, 345-350 (2018).
Buß, Maren, Geerds, Christina, Patschkowski, Thomas, Niehaus, Karsten, and Niemann, Hartmut. “Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris”. Acta Crystallographica Section F Structural Biology Communications 74.6 (2018): 345-350.

Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

36 References

Daten bereitgestellt von Europe PubMed Central.

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH., Acta Crystallogr. D Biol. Crystallogr. 66(Pt 2), 2010
PMID: 20124702
Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data.
Alkhateeb RS, Ruckert C, Rupp O, Pucker B, Hublik G, Wibberg D, Niehaus K, Puhler A, Vorholter FJ., J. Biotechnol. 253(), 2017
PMID: 28506932
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.
Alva V, Nam SZ, Soding J, Lupas AN., Nucleic Acids Res. 44(W1), 2016
PMID: 27131380
The structure of flavin-dependent tryptophan 7-halogenase RebH.
Bitto E, Huang Y, Bingman CA, Singh S, Thorson JS, Phillips GN Jr., Proteins 70(1), 2008
PMID: 17876823
Structure and action of the myxobacterial chondrochloren halogenase CndH: a new variant of FAD-dependent halogenases.
Buedenbender S, Rachid S, Muller R, Schulz GE., J. Mol. Biol. 385(2), 2008
PMID: 19000696
Twinned crystals and anomalous phasing.
Dauter Z., Acta Crystallogr. D Biol. Crystallogr. 59(Pt 11), 2003
PMID: 14573956
Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination.
Dong C, Flecks S, Unversucht S, Haupt C, van Pee KH, Naismith JH., Science 309(5744), 2005
PMID: 16195462
Biosynthesis of coral settlement cue tetrabromopyrrole in marine bacteria by a uniquely adapted brominase-thioesterase enzyme pair.
El Gamal A, Agarwal V, Diethelm S, Rahman I, Schorn MA, Sneed JM, Louie GV, Whalen KE, Mincer TJ, Noel JP, Paul VJ, Moore BS., Proc. Natl. Acad. Sci. U.S.A. 113(14), 2016
PMID: 27001835
Features and development of Coot.
Emsley P, Lohkamp B, Scott WG, Cowtan K., Acta Crystallogr. D Biol. Crystallogr. 66(Pt 4), 2010
PMID: 20383002
Function and Structure of MalA/MalA', Iterative Halogenases for Late-Stage C-H Functionalization of Indole Alkaloids.
Fraley AE, Garcia-Borras M, Tripathi A, Khare D, Mercado-Marin EV, Tran H, Dan Q, Webb GP, Watts KR, Crews P, Sarpong R, Williams RM, Smith JL, Houk KN, Sherman DH., J. Am. Chem. Soc. 139(34), 2017
PMID: 28777910
Enzymatic halogenation of tryptophan on a gram scale.
Frese M, Sewald N., Angew. Chem. Int. Ed. Engl. 54(1), 2014
PMID: 25394328

AUTHOR UNKNOWN, 0
XDS.
Kabsch W., Acta Crystallogr. D Biol. Crystallogr. 66(Pt 2), 2010
PMID: 20124692
Solution of the structure of a calmodulin-peptide complex in a novel configuration from a variably twinned data set.
Keller JP., Acta Crystallogr D Struct Biol 73(Pt 1), 2017
PMID: 28045382
Development of Halogenase Enzymes for Use in Synthesis.
Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J., Chem. Rev. 118(1), 2017
PMID: 28466644
Intensity statistics in twinned crystals with examples from the PDB.
Lebedev AA, Vagin AA, Murshudov GN., Acta Crystallogr. D Biol. Crystallogr. 62(Pt 1), 2005
PMID: 16369097
Phaser crystallographic software.
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ., J Appl Crystallogr 40(Pt 4), 2007
PMID: 19461840
Experimental phasing: best practice and pitfalls.
McCoy AJ, Read RJ., Acta Crystallogr. D Biol. Crystallogr. 66(Pt 4), 2010
PMID: 20382999
RadH: A Versatile Halogenase for Integration into Synthetic Pathways.
Menon BRK, Brandenburger E, Sharif HH, Klemstein U, Shepherd SA, Greaney MF, Micklefield J., Angew. Chem. Int. Ed. Engl. 56(39), 2017
PMID: 28722773
Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis.
Ortega MA, Cogan DP, Mukherjee S, Garg N, Li B, Thibodeaux GN, Maffioli SI, Donadio S, Sosio M, Escano J, Smith L, Nair SK, van der Donk WA., ACS Chem. Biol. 12(2), 2017
PMID: 28032983
Crystal structure of halogenase PltA from the pyoluteorin biosynthetic pathway.
Pang AH, Garneau-Tsodikova S, Tsodikov OV., J. Struct. Biol. 192(3), 2015
PMID: 26416533
Chloramphenicol biosynthesis: the structure of CmlS, a flavin-dependent halogenase showing a covalent flavin-aspartate bond.
Podzelinska K, Latimer R, Bhattacharya A, Vining LC, Zechel DL, Jia Z., J. Mol. Biol. 397(1), 2010
PMID: 20080101
Tetartohedral twinning could happen to you too.
Roversi P, Blanc E, Johnson S, Lea SM., Acta Crystallogr. D Biol. Crystallogr. 68(Pt 4), 2012
PMID: 22505261
Use of multiple anomalous dispersion to phase highly merohedrally twinned crystals of interleukin-1beta.
Rudolph MG, Kelker MS, Schneider TR, Yeates TO, Oseroff V, Heidary DK, Jennings PA, Wilson IA., Acta Crystallogr. D Biol. Crystallogr. 59(Pt 2), 2003
PMID: 12554939
An Unusual Flavin-Dependent Halogenase from the Metagenome of the Marine Sponge Theonella swinhoei WA.
Smith DRM, Uria AR, Helfrich EJN, Milbredt D, van Pee KH, Piel J, Goss RJM., ACS Chem. Biol. 12(5), 2017
PMID: 28198609
The unusual extended C-terminal helix of the peroxisomal α/β-hydrolase Lpx1 is involved in dimer contacts but dispensable for dimerization.
Thoms S, Hofhuis J, Thoing C, Gartner J, Niemann HH., J. Struct. Biol. 175(3), 2011
PMID: 21741480
Molecular replacement with MOLREP.
Vagin A, Teplyakov A., Acta Crystallogr. D Biol. Crystallogr. 66(Pt 1), 2009
PMID: 20057045
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Vorholter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Ruckert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Puhler A., J. Biotechnol. 134(1-2), 2008
PMID: 18304669
Specific Enzymatic Halogenation-From the Discovery of Halogenated Enzymes to Their Applications In Vitro and In Vivo.
Weichold V, Milbredt D, van Pee KH., Angew. Chem. Int. Ed. Engl. 55(22), 2016
PMID: 27059664
Overview of the CCP4 suite and current developments.
Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS., Acta Crystallogr. D Biol. Crystallogr. 67(Pt 4), 2011
PMID: 21460441
Effects of crystal twinning on the ability to solve a macromolecular structure using multiwavelength anomalous diffraction.
Yang F, Dauter Z, Wlodawer A., Acta Crystallogr. D Biol. Crystallogr. 56(Pt 8), 2000
PMID: 10944332
Chlorination by a long-lived intermediate in the mechanism of flavin-dependent halogenases.
Yeh E, Blasiak LC, Koglin A, Drennan CL, Walsh CT., Biochemistry 46(5), 2007
PMID: 17260957
A regioselective tryptophan 5-halogenase is involved in pyrroindomycin biosynthesis in Streptomyces rugosporus LL-42D005.
Zehner S, Kotzsch A, Bister B, Sussmuth RD, Mendez C, Salas JA, van Pee KH., Chem. Biol. 12(4), 2005
PMID: 15850981
A novel fungal flavin-dependent halogenase for natural product biosynthesis.
Zeng J, Zhan J., Chembiochem 11(15), 2010
PMID: 20827793
Structural insights into regioselectivity in the enzymatic chlorination of tryptophan.
Zhu X, De Laurentis W, Leang K, Herrmann J, Ihlefeld K, van Pee KH, Naismith JH., J. Mol. Biol. 391(1), 2009
PMID: 19501593
Surprises and pitfalls arising from (pseudo)symmetry.
Zwart PH, Grosse-Kunstleve RW, Lebedev AA, Murshudov GN, Adams PD., Acta Crystallogr. D Biol. Crystallogr. 64(Pt 1), 2007
PMID: 18094473
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 29870018
PubMed | Europe PMC

Suchen in

Google Scholar