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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.
SigmaS-transcription initiation complex with 4-nt nascent RNA

Results of the assignment of 66 detected steps in 1 model(s), can be also downloaded as csv file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
015ipn_1_DC27_DA28BBBBB00370.33BB00
025ipn_1_DA28_DC29BBBBB00650.27BB00
035ipn_1_DC29_DG30BBBBB00420.21BB00
045ipn_1_DG30_DT31BBBBB00670.24BB00
055ipn_1_DT31_DA32BB1BB02260.27BB02
065ipn_1_DA32_DT33BBBBB00460.35BB00
075ipn_1_DT33_DG34BB1BB02210.22BB02
085ipn_1_DG34_DC35B12BB04630.26BB04
095ipn_1_DC35_DT36B12BB04260.24BB04
105ipn_1_DT36_DA37OPNOP20540.46OP20
115ipn_1_DA37_DT38NANNANT00.82OP13
125ipn_1_DT38_DA39BBBBB00380.57BB00
135ipn_1_DA39_DA40BBBBB00700.23BB00
145ipn_1_DA40_DT41NANNANT00.70OP20
155ipn_1_DT41_DG42NANNANT01.48IC03
165ipn_1_DG42_DT43NANNANT00.70IC05
175ipn_1_DT43_DG44NANNANT00.80BB00
185ipn_1_DG44_DT45NANNANT01.73BA09
195ipn_1_DT45_DG46NANNANT01.30BB08
205ipn_1_DG46_DC47NANNANT00.71BB13
215ipn_1_DC47_DA48NANNANT00.64BB10
225ipn_1_DA48_DG49NANNANT00.78BA09
235ipn_1_DG49_DT50NANNANT00.90AB02
245ipn_1_DT50_DC51NANNANT01.60OP11
255ipn_1_DC51_DT52BBBBB00230.44BB00
265ipn_1_DT52_DG53B12BB04890.18BB04
275ipn_1_DG53_DA54BB1BB02580.18BB02
285ipn_1_DA54_DC55BBBBB00720.20BB00
295ipn_1_DC55_DG56BB2BB08280.45BB08
305ipn_1_DG56_DC57BBBBB00720.26BB00
315ipn_1_DC57_DG58NANNANT00.63BB03
325ipn_1_DG58_DG59NANNANT00.52BB11
335ipn_2_DC4_DC5NANNANT00.58BB02
345ipn_2_DC5_DG6BBBBB00260.40BB00
355ipn_2_DG6_DC7B-ABA08530.33BA08
365ipn_2_DC7_DG8BBBBB00130.29BB00
375ipn_2_DG8_DT9miBBB15690.20BB15
385ipn_2_DT9_DC10B-ABA05420.33BA05
395ipn_2_DC10_DA11AA1AA01180.51AA01
405ipn_2_DA11_DG12AAAAA08370.23AA08
415ipn_2_DG12_DA13NANNANT01.07OP05
425ipn_2_DA13_DC14AAAAA00590.27AA00
435ipn_2_DC14_DT15AA1AA06300.28AA06
445ipn_2_DT15_DC16NANNANT00.47AA06
455ipn_2_DC16_DG17NANNANT00.72AA11
465ipn_2_DG17_DT18NANNANT00.35AA03
475ipn_2_DT18_DA19AAAAA09780.30AA09
485ipn_2_DA19_DG20NANNANT00.89BB08
495ipn_2_DG20_DG21BB1BB02210.37BB02
505ipn_2_DG21_DA22NANNANT00.88BB00
515ipn_2_DT23_DT24NANNANT00.33BB02
525ipn_2_DT24_DA25NANNANT00.40BB10
535ipn_2_DA25_DT26NANNANT00.63BA10
545ipn_2_DT26_DA27NANNANT00.66OP06
555ipn_2_DA27_DG28BBBBB00670.49BB00
565ipn_2_DG28_DC29BBBBB00840.24BB00
575ipn_2_DC29_DA30BBBBB00810.25BB00
585ipn_2_DA30_DT31BBBBB00810.23BB00
595ipn_2_DT31_DA32BBBBB00750.18BB00
605ipn_2_DA32_DC33BBBBB00850.16BB00
615ipn_2_DC33_DG34BBBBB00780.18BB00
625ipn_2_DG34_DT35BBBBB00270.30BB00
635ipn_2_DT35_DG36B12BB04660.27BB04
645ipn_3_GTP14_A15AA2AA12600.44AA12
655ipn_3_A15_G16NANNANT00.55AA10
665ipn_3_G16_U17NANNANT00.58AA10

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

© Jiří Černý & Bohdan Schneider

Definition of torsion angles
step:
Table of conformers

δεζα1β1γ1δ1χχ1NCCNNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Drag the plot for panning, scroll to zoom, click a point to show superposition in JSmol.

Download

Results (as csv)
Restraints (default edits file)
Best NtC fitted to input structure.

Definition of the conformers as torsion averages (csv) and their esd values (csv) or as their Cartesian coordinates of the conformers

Download the papers:

description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
example of application:
Schneider et al., Genes, 8(10), 278, (2017).

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