About: X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase

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Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://www.sciencedirect.com/science/article/pii/S1047847714001373
Description	The crystal structure of the N-terminal domain of the RNA polymerase delta subunit (Ndelta) from Bacillus subtilis solved at a resolution of 2.0 A is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important beta sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Ndelta, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni2+ ions, are the main reason for such a difference. The crystal structure of the N-terminal domain of the RNA polymerase delta subunit (Ndelta) from Bacillus subtilis solved at a resolution of 2.0 A is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure exhibits significant differences from the lowest energy NMR structure. In addition to the overall structure differences, structurally important beta sheets found in the NMR structure are not present in the crystal structure. We systematically investigated the cause of the discrepancies between the NMR and X-ray structures of Ndelta, addressing the pH dependence, presence of metal ions, and crystal packing forces. We convincingly showed that the crystal packing forces, together with the presence of Ni2+ ions, are the main reason for such a difference. (en)
Title	X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase (en)
skos:prefLabel	X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase (en)
skos:notation	RIV/00216224:14740/14:00073722!RIV15-MSM-14740___
http://linked.open...avai/riv/aktivita	I P S
http://linked.open...avai/riv/aktivity	I, P(ED1.1.00/02.0068), P(EE2.3.30.0009), P(GA13-16842S), S
http://linked.open...iv/cisloPeriodika	2
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Komárek, Jan Demo, Gabriel Sklenář, Vladimír Kadeřávek, Pavel Žídek, Lukáš Wimmerová, Michaela Papoušková, Veronika Srb, Pavel Třísková, Olga
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Středoevropský technologický institut
http://linked.open...dnocenehoVysledku	56472
http://linked.open...ai/riv/idVysledku	RIV/00216224:14740/14:00073722
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	N-terminal domain; Nuclear magnetic resonance; Protein crystallography; RNA polymerase; delta-Subunit (en)
http://linked.open.../riv/klicoveSlovo	RNA polymerase N-terminal domain Nuclear magnetic resonance delta-Subunit Protein crystallography
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[B5F2C139E380]
http://linked.open...i/riv/nazevZdroje	Journal of Structural Biology
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	9 (xsd:int)
http://linked.open...cetTvurcuVysledku	11 (xsd:int)
http://linked.open...vavai/riv/projekt	PODJEDNOTKY URČUJÍCÍ DNA SPECIFICITU BAKTERIÁLNÍ RNA POLYMERÁZY S FLEXIBILNÍMI DOMÉNAMI: FUNKCE A DYNAMIKA Central european institute of technology Employment of Newly Graduated Doctors of Science for Scientific Excellence
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	187
http://linked.open...iv/tvurceVysledku	Demo, Gabriel Kadeřávek, Pavel Krásný, Libor Komárek, Jan Papoušková, Veronika Sklenář, Vladimír Wimmerová, Michaela Žídek, Lukáš Srb, Pavel Otrusinová, Olga Rabatinova, Alzbeta
http://linked.open...ain/vavai/riv/wos	000340217300008
issn	1047-8477
number of pages	13 (xsd:int)
http://bibframe.org/vocab/doi	10.1016/j.jsb.2014.06.001
http://localhost/t...ganizacniJednotka	14740

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