DNATCO v3.2: results

Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.

Results of the assignment of 54 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.

step number	Step name	CANA	NtC	confal	rmsd
01	2bh2_C_A1932_G1933	AAA	AA08	70	0.45	AA08
02	2bh2_C_G1933_C1934	AAA	AA00	47	0.36	AA00
03	2bh2_C_C1934_G1935	AAA	AA08	69	0.38	AA08
04	2bh2_C_G1935_A1936	AAA	AA08	52	0.22	AA08
05	2bh2_C_A1936_A1937	NAN	NANT	0	2.27	IC04
06	2bh2_C_A1937_A1938	NAN	NANT	0	1.11	OP06
07	2bh2_C_U1940_C1941	AAA	AA00	74	0.30	AA00
08	2bh2_C_C1941_C1942	AAA	AA08	40	0.60	AA08
09	2bh2_C_C1942_U1943	NAN	NANT	0	0.81	OP06
10	2bh2_C_U1943_U1944	NAN	NANT	0	1.29	OP17
11	2bh2_C_U1944_G1945	AAA	AA08	40	0.35	AA08
12	2bh2_C_G1945_U1946	AAA	AA00	86	0.09	AA00
13	2bh2_C_U1946_C1947	AAA	AA00	75	0.11	AA00
14	2bh2_C_C1947_G1948	AAA	AA00	73	0.15	AA00
15	2bh2_C_G1948_G1949	AAA	AA00	71	0.19	AA00
16	2bh2_C_G1949_G1950	AAA	AA00	62	0.34	AA00
17	2bh2_C_G1950_U1951	AAA	AA08	64	0.24	AA08
18	2bh2_C_U1951_A1952	NAN	NANT	0	0.72	OP09
19	2bh2_C_A1952_A1953	NAN	NANT	0	0.72	OP14
20	2bh2_C_A1953_G1954	NAN	NANT	0	0.68	OP20
21	2bh2_C_G1954_U1955	NAN	NANT	0	1.23	BB10
22	2bh2_C_U1955_U1956	A-B	AB04	29	0.57	AB04
23	2bh2_C_U1956_C1957	OPN	OP12	27	0.58	OP12
24	2bh2_C_C1957_C1958	AAA	AA08	72	0.18	AA08
25	2bh2_C_C1958_G1959	AAA	AA03	62	0.24	AA03
26	2bh2_C_G1959_A1960	AAA	AA00	64	0.19	AA00
27	2bh2_C_A1960_C1961	AAA	AA00	77	0.12	AA00
28	2bh2_D_A1932_G1933	AAA	AA00	78	0.25	AA00
29	2bh2_D_G1933_C1934	AAA	AA08	62	0.37	AA08
30	2bh2_D_C1934_G1935	AAA	AA08	63	0.39	AA08
31	2bh2_D_G1935_A1936	AAA	AA08	79	0.20	AA08
32	2bh2_D_A1936_A1937	NAN	NANT	0	0.82	OP30
33	2bh2_D_A1937_A1938	NAN	NANT	0	1.20	OP06
34	2bh2_D_U1940_C1941	AAA	AA04	86	0.28	AA04
35	2bh2_D_C1941_C1942	AAA	AA08	28	0.62	AA08
36	2bh2_D_C1942_U1943	NAN	NANT	0	0.96	OP01
37	2bh2_D_U1943_U1944	NAN	NANT	0	1.27	OP17
38	2bh2_D_U1944_G1945	NAN	NANT	0	0.56	AA08
39	2bh2_D_G1945_U1946	AAA	AA00	26	0.32	AA00
40	2bh2_D_U1946_C1947	AAA	AA08	38	0.29	AA08
41	2bh2_D_C1947_G1948	AAA	AA04	85	0.22	AA04
42	2bh2_D_G1948_G1949	AAA	AA00	60	0.25	AA00
43	2bh2_D_G1949_G1950	AAA	AA04	81	0.28	AA04
44	2bh2_D_G1950_U1951	AAA	AA08	60	0.25	AA08
45	2bh2_D_U1951_A1952	NAN	NANT	0	0.85	OP09
46	2bh2_D_A1952_A1953	NAN	NANT	0	1.95	OP06
47	2bh2_D_A1953_G1954	NAN	NANT	0	0.72	OP20
48	2bh2_D_G1954_U1955	OPN	OP15	35	0.52	OP15
49	2bh2_D_U1955_U1956	NAN	NANT	0	0.54	AB04
50	2bh2_D_U1956_C1957	OPN	OP12	46	0.49	OP12
51	2bh2_D_C1957_C1958	AAA	AA00	66	0.19	AA00
52	2bh2_D_C1958_G1959	AAA	AA00	75	0.14	AA00
53	2bh2_D_G1959_A1960	NAN	NANT	0	0.56	AA10
54	2bh2_D_A1960_C1961	AAA	AA08	38	0.37	AA08

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

step:
Table of conformers

δ1

ε1

ζ1

α2

β2

γ2

δ2

χ1

χ2

μ

NN

CC

step_torsions

ntC_average

Δ torsions

torsion scores

comments step confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

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).

Browse conformers

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A-B

B-A

B

IC

OPN

Z

N

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