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Conformers: ABBIImiBZICOPNSYNN
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Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe

Results of the assignment of 69 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.
step numberStep nameCANANtCconfalrmsd
016y4b_F_G1_C2AAAAA08600.27 AA08
026y4b_F_C2_C3AAAAA00720.12 AA00
036y4b_F_C3_C4AAAAA00530.28 AA00
046y4b_F_C4_G5AAwAA01130.49 AA01
056y4b_F_G5_G6AAwAA01310.35 AA01
066y4b_F_G6_A7A-BAB05610.35 AB05
076y4b_F_A7_4SU8NANNANT01.61 OP13
086y4b_F_4SU8_A9NANNANT00.85 IC03
096y4b_F_A9_G10NANNANT01.25 OP12
106y4b_F_G10_C11AAAAA08480.31 AA08
116y4b_F_C11_U12AAAAA00800.18 AA00
126y4b_F_U12_C13AAwAA11610.45 AA11
136y4b_F_C13_A14AAAAA00520.19 AA00
146y4b_F_A14_G15NANNANT00.52 AA06
156y4b_F_G15_H2U16NANNANT01.32 OP1S
166y4b_F_H2U16_C17NANNANT01.52 OP31
176y4b_F_C17_G18NANNANT00.96 ZZS2
186y4b_F_G18_G19BB2BB07210.44 BB07
196y4b_F_G19_H2U20NANNANT02.04 OP17
206y4b_F_H2U20_A21NANNANT01.25 OP06
216y4b_F_A21_G22NANNANT00.82 AB05
226y4b_F_G22_A23NANNANT00.56 BA13
236y4b_F_A23_G24AAAAA00650.14 AA00
246y4b_F_G24_C25AAAAA08820.23 AA08
256y4b_F_C25_A26AAAAA08640.35 AA08
266y4b_F_A26_G27AAAAA08440.29 AA08
276y4b_F_G27_G28AAAAA00290.33 AA00
286y4b_F_G28_G29AAAAA00750.16 AA00
296y4b_F_G29_G30NANNANT00.57 AA11
306y4b_F_G30_A31AAAAA08370.35 AA08
316y4b_F_U33_G34NANNANT00.38 OP04
326y4b_F_G34_A35AAAAA08640.37 AA08
336y4b_F_A35_A36AAwAA11880.11 AA11
346y4b_F_A36_A37AAAAA08450.31 AA08
356y4b_F_A37_A38NANNANT00.98 IC04
366y4b_F_C40_C41AAAAA08840.18 AA08
376y4b_F_C41_C42AAAAA08680.26 AA08
386y4b_F_C42_C43AAAAA08730.24 AA08
396y4b_F_C43_G44ICLIC01590.25 IC01
406y4b_F_G44_U45NANNANT00.92 OP13
416y4b_F_U45_G46NANNANT02.56 OP24
426y4b_F_G46_U47NANNANT01.54 OP05
436y4b_F_U47_C48NANNANT00.97 OP11
446y4b_F_C48_C49NANNANT01.37 OP05
456y4b_F_C49_U50NANNANT00.42 AA06
466y4b_F_U50_U51AAAAA04720.38 AA04
476y4b_F_U51_G52AAwAA01340.51 AA01
486y4b_F_G52_G53NANNANT00.55 AA01
496y4b_F_G53_5MU54AAAAA08200.40 AA08
506y4b_F_C56_G57AAAAA08940.29 AA08
516y4b_F_G57_A58NANNANT00.74 AB05
526y4b_F_A58_U59NANNANT00.77 OP14
536y4b_F_U59_U60NANNANT00.99 AA04
546y4b_F_U60_C61NANNANT01.74 OP10
556y4b_F_C61_C62AAAAA04440.50 AA04
566y4b_F_C62_G63AAAAA00340.30 AA00
576y4b_F_G63_A64AAAAA00710.12 AA00
586y4b_F_A64_G65AAwAA06740.21 AA06
596y4b_F_G65_U66AAAAA03160.46 AA03
606y4b_F_U66_C67AAAAA00840.11 AA00
616y4b_F_C67_C68AAwAA01240.40 AA01
626y4b_F_C68_G69NANNANT00.52 AA10
636y4b_F_G69_G70AAAAA00590.32 AA00
646y4b_F_G70_G71AAAAA00560.28 AA00
656y4b_F_G71_C72AAwAA01680.24 AA01
666y4b_F_C72_A73AAwAA06790.44 AA06
676y4b_F_A73_C74NANNANT00.76 AA10
686y4b_F_C74_C75NANNANT01.55 AA10
696y4b_F_C75_A76NANNANT01.09 AA06

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
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

Download

Results as csv or json file.
Best NtC fitted to input structure.

Restraints

Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Restraints file for Phenix (steps with RMSD <= 0.5Å) [?]

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of 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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