PDB-4s1f: Fructose-6-phosphate aldolase A from E.coli soaked in acetylacetone

Basic information

• Entry: Database: PDB / ID: 4s1f
• Title: Fructose-6-phosphate aldolase A from E.coli soaked in acetylacetone
• Components: Fructose-6-phosphate aldolase 1
• Keywords: LYASE / Modification of active Lys85 by acetylacetone / Tim barrel / homodecamer / Fructose-6-phosphate aldolase A / Cytosol

Function / homology

Function:

ketone catabolic process / fructose 6-phosphate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / fructose metabolic process / identical protein binding / cytoplasm

Domain/homology:

Fructose-6-phosphate aldolase / Transaldolase type 3B/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase, archaeal/bacterial / Transaldolase active site. / Transaldolase, active site / Transaldolase signature 1. / Transaldolase/Fructose-6-phosphate aldolase / Transaldolase/Fructose-6-phosphate aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta

Component:

pentane-2,4-dione / Fructose-6-phosphate aldolase 1

• Biological species: Escherichia coli (E. coli)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.242 Å
• Authors: Stellmacher, L. / Sandalova, T. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.
• Citation: Journal: ChemCatChem / Year: 2015; Title: Acid Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase; Authors: Stellmacher, L. / Sandalova, T. / Leptihn, S. / Schneider, G. / Sprenger, G.A. / Samland, A.K.

History

Deposition	Jan 13, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 7, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Assembly

Deposited unit

A: Fructose-6-phosphate aldolase 1

B: Fructose-6-phosphate aldolase 1

C: Fructose-6-phosphate aldolase 1

D: Fructose-6-phosphate aldolase 1

E: Fructose-6-phosphate aldolase 1

F: Fructose-6-phosphate aldolase 1

G: Fructose-6-phosphate aldolase 1

H: Fructose-6-phosphate aldolase 1

I: Fructose-6-phosphate aldolase 1

J: Fructose-6-phosphate aldolase 1

K: Fructose-6-phosphate aldolase 1

L: Fructose-6-phosphate aldolase 1

M: Fructose-6-phosphate aldolase 1

N: Fructose-6-phosphate aldolase 1

O: Fructose-6-phosphate aldolase 1

P: Fructose-6-phosphate aldolase 1

Q: Fructose-6-phosphate aldolase 1

R: Fructose-6-phosphate aldolase 1

S: Fructose-6-phosphate aldolase 1

T: Fructose-6-phosphate aldolase 1

hetero molecules

Summary:

• 477 kDa, 20 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	477,413	25
Polymers	476,913	20
Non-polymers	501	5
Water	13,421	745

1

A: Fructose-6-phosphate aldolase 1

B: Fructose-6-phosphate aldolase 1

C: Fructose-6-phosphate aldolase 1

D: Fructose-6-phosphate aldolase 1

E: Fructose-6-phosphate aldolase 1

F: Fructose-6-phosphate aldolase 1

G: Fructose-6-phosphate aldolase 1

H: Fructose-6-phosphate aldolase 1

I: Fructose-6-phosphate aldolase 1

J: Fructose-6-phosphate aldolase 1

hetero molecules

Summary:

• defined by author&software
• 239 kDa, 10 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	238,757	13
Polymers	238,456	10
Non-polymers	300	3
Water	180	10

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	38780 Å2
ΔGint	-319 kcal/mol
Surface area	69960 Å2
Method	PISA

2

K: Fructose-6-phosphate aldolase 1

L: Fructose-6-phosphate aldolase 1

M: Fructose-6-phosphate aldolase 1

N: Fructose-6-phosphate aldolase 1

O: Fructose-6-phosphate aldolase 1

P: Fructose-6-phosphate aldolase 1

Q: Fructose-6-phosphate aldolase 1

R: Fructose-6-phosphate aldolase 1

S: Fructose-6-phosphate aldolase 1

T: Fructose-6-phosphate aldolase 1

hetero molecules

Summary:

• defined by author&software
• 239 kDa, 10 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	238,657	12
Polymers	238,456	10
Non-polymers	200	2
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	38800 Å2
ΔGint	-316 kcal/mol
Surface area	70000 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	100.485, 130.709, 355.180
Angle α, β, γ (deg.)	90.00, 90.21, 90.00
Int Tables number	5
Space group name H-M	I121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	A
2	12	M
1	13	A
2	13	N
1	14	A
2	14	O
1	15	A
2	15	P
1	16	A
2	16	Q
1	17	A
2	17	R
1	18	A
2	18	S
1	19	A
2	19	T
1	20	B
2	20	C
1	21	B
2	21	D
1	22	B
2	22	E
1	23	B
2	23	F
1	24	B
2	24	G
1	25	B
2	25	H
1	26	B
2	26	I
1	27	B
2	27	J
1	28	B
2	28	K
1	29	B
2	29	L
1	30	B
2	30	M
1	31	B
2	31	N
1	32	B
2	32	O
1	33	B
2	33	P
1	34	B
2	34	Q
1	35	B
2	35	R
1	36	B
2	36	S
1	37	B
2	37	T
1	38	C
2	38	D
1	39	C
2	39	E
1	40	C
2	40	F
1	41	C
2	41	G
1	42	C
2	42	H
1	43	C
2	43	I
1	44	C
2	44	J
1	45	C
2	45	K
1	46	C
2	46	L
1	47	C
2	47	M
1	48	C
2	48	N
1	49	C
2	49	O
1	50	C
2	50	P
1	51	C
2	51	Q
1	52	C
2	52	R
1	53	C
2	53	S
1	54	C
2	54	T
1	55	D
2	55	E
1	56	D
2	56	F
1	57	D
2	57	G
1	58	D
2	58	H
1	59	D
2	59	I
1	60	D
2	60	J
1	61	D
2	61	K
1	62	D
2	62	L
1	63	D
2	63	M
1	64	D
2	64	N
1	65	D
2	65	O
1	66	D
2	66	P
1	67	D
2	67	Q
1	68	D
2	68	R
1	69	D
2	69	S
1	70	D
2	70	T
1	71	E
2	71	F
1	72	E
2	72	G
1	73	E
2	73	H
1	74	E
2	74	I
1	75	E
2	75	J
1	76	E
2	76	K
1	77	E
2	77	L
1	78	E
2	78	M
1	79	E
2	79	N
1	80	E
2	80	O
1	81	E
2	81	P
1	82	E
2	82	Q
1	83	E
2	83	R
1	84	E
2	84	S
1	85	E
2	85	T
1	86	F
2	86	G
1	87	F
2	87	H
1	88	F
2	88	I
1	89	F
2	89	J
1	90	F
2	90	K
1	91	F
2	91	L
1	92	F
2	92	M
1	93	F
2	93	N
1	94	F
2	94	O
1	95	F
2	95	P
1	96	F
2	96	Q
1	97	F
2	97	R
1	98	F
2	98	S
1	99	F
2	99	T
1	100	G
2	100	H
1	101	G
2	101	I
1	102	G
2	102	J
1	103	G
2	103	K
1	104	G
2	104	L
1	105	G
2	105	M
1	106	G
2	106	N
1	107	G
2	107	O
1	108	G
2	108	P
1	109	G
2	109	Q
1	110	G
2	110	R
1	111	G
2	111	S
1	112	G
2	112	T
1	113	H
2	113	I
1	114	H
2	114	J
1	115	H
2	115	K
1	116	H
2	116	L
1	117	H
2	117	M
1	118	H
2	118	N
1	119	H
2	119	O
1	120	H
2	120	P
1	121	H
2	121	Q
1	122	H
2	122	R
1	123	H
2	123	S
1	124	H
2	124	T
1	125	I
2	125	J
1	126	I
2	126	K
1	127	I
2	127	L
1	128	I
2	128	M
1	129	I
2	129	N
1	130	I
2	130	O
1	131	I
2	131	P
1	132	I
2	132	Q
1	133	I
2	133	R
1	134	I
2	134	S
1	135	I
2	135	T
1	136	J
2	136	K
1	137	J
2	137	L
1	138	J
2	138	M
1	139	J
2	139	N
1	140	J
2	140	O
1	141	J
2	141	P
1	142	J
2	142	Q
1	143	J
2	143	R
1	144	J
2	144	S
1	145	J
2	145	T
1	146	K
2	146	L
1	147	K
2	147	M
1	148	K
2	148	N
1	149	K
2	149	O
1	150	K
2	150	P
1	151	K
2	151	Q
1	152	K
2	152	R
1	153	K
2	153	S
1	154	K
2	154	T
1	155	L
2	155	M
1	156	L
2	156	N
1	157	L
2	157	O
1	158	L
2	158	P
1	159	L
2	159	Q
1	160	L
2	160	R
1	161	L
2	161	S
1	162	L
2	162	T
1	163	M
2	163	N
1	164	M
2	164	O
1	165	M
2	165	P
1	166	M
2	166	Q
1	167	M
2	167	R
1	168	M
2	168	S
1	169	M
2	169	T
1	170	N
2	170	O
1	171	N
2	171	P
1	172	N
2	172	Q
1	173	N
2	173	R
1	174	N
2	174	S
1	175	N
2	175	T
1	176	O
2	176	P
1	177	O
2	177	Q
1	178	O
2	178	R
1	179	O
2	179	S
1	180	O
2	180	T
1	181	P
2	181	Q
1	182	P
2	182	R
1	183	P
2	183	S
1	184	P
2	184	T
1	185	Q
2	185	R
1	186	Q
2	186	S
1	187	Q
2	187	T
1	188	R
2	188	S
1	189	R
2	189	T
1	190	S
2	190	T

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 220 / Label seq-ID: 7 - 226

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	A	A
2	12	M	M
1	13	A	A
2	13	N	N
1	14	A	A
2	14	O	O
1	15	A	A
2	15	P	P
1	16	A	A
2	16	Q	Q
1	17	A	A
2	17	R	R
1	18	A	A
2	18	S	S
1	19	A	A
2	19	T	T
1	20	B	B
2	20	C	C
1	21	B	B
2	21	D	D
1	22	B	B
2	22	E	E
1	23	B	B
2	23	F	F
1	24	B	B
2	24	G	G
1	25	B	B
2	25	H	H
1	26	B	B
2	26	I	I
1	27	B	B
2	27	J	J
1	28	B	B
2	28	K	K
1	29	B	B
2	29	L	L
1	30	B	B
2	30	M	M
1	31	B	B
2	31	N	N
1	32	B	B
2	32	O	O
1	33	B	B
2	33	P	P
1	34	B	B
2	34	Q	Q
1	35	B	B
2	35	R	R
1	36	B	B
2	36	S	S
1	37	B	B
2	37	T	T
1	38	C	C
2	38	D	D
1	39	C	C
2	39	E	E
1	40	C	C
2	40	F	F
1	41	C	C
2	41	G	G
1	42	C	C
2	42	H	H
1	43	C	C
2	43	I	I
1	44	C	C
2	44	J	J
1	45	C	C
2	45	K	K
1	46	C	C
2	46	L	L
1	47	C	C
2	47	M	M
1	48	C	C
2	48	N	N
1	49	C	C
2	49	O	O
1	50	C	C
2	50	P	P
1	51	C	C
2	51	Q	Q
1	52	C	C
2	52	R	R
1	53	C	C
2	53	S	S
1	54	C	C
2	54	T	T
1	55	D	D
2	55	E	E
1	56	D	D
2	56	F	F
1	57	D	D
2	57	G	G
1	58	D	D
2	58	H	H
1	59	D	D
2	59	I	I
1	60	D	D
2	60	J	J
1	61	D	D
2	61	K	K
1	62	D	D
2	62	L	L
1	63	D	D
2	63	M	M
1	64	D	D
2	64	N	N
1	65	D	D
2	65	O	O
1	66	D	D
2	66	P	P
1	67	D	D
2	67	Q	Q
1	68	D	D
2	68	R	R
1	69	D	D
2	69	S	S
1	70	D	D
2	70	T	T
1	71	E	E
2	71	F	F
1	72	E	E
2	72	G	G
1	73	E	E
2	73	H	H
1	74	E	E
2	74	I	I
1	75	E	E
2	75	J	J
1	76	E	E
2	76	K	K
1	77	E	E
2	77	L	L
1	78	E	E
2	78	M	M
1	79	E	E
2	79	N	N
1	80	E	E
2	80	O	O
1	81	E	E
2	81	P	P
1	82	E	E
2	82	Q	Q
1	83	E	E
2	83	R	R
1	84	E	E
2	84	S	S
1	85	E	E
2	85	T	T
1	86	F	F
2	86	G	G
1	87	F	F
2	87	H	H
1	88	F	F
2	88	I	I
1	89	F	F
2	89	J	J
1	90	F	F
2	90	K	K
1	91	F	F
2	91	L	L
1	92	F	F
2	92	M	M
1	93	F	F
2	93	N	N
1	94	F	F
2	94	O	O
1	95	F	F
2	95	P	P
1	96	F	F
2	96	Q	Q
1	97	F	F
2	97	R	R
1	98	F	F
2	98	S	S
1	99	F	F
2	99	T	T
1	100	G	G
2	100	H	H
1	101	G	G
2	101	I	I
1	102	G	G
2	102	J	J
1	103	G	G
2	103	K	K
1	104	G	G
2	104	L	L
1	105	G	G
2	105	M	M
1	106	G	G
2	106	N	N
1	107	G	G
2	107	O	O
1	108	G	G
2	108	P	P
1	109	G	G
2	109	Q	Q
1	110	G	G
2	110	R	R
1	111	G	G
2	111	S	S
1	112	G	G
2	112	T	T
1	113	H	H
2	113	I	I
1	114	H	H
2	114	J	J
1	115	H	H
2	115	K	K
1	116	H	H
2	116	L	L
1	117	H	H
2	117	M	M
1	118	H	H
2	118	N	N
1	119	H	H
2	119	O	O
1	120	H	H
2	120	P	P
1	121	H	H
2	121	Q	Q
1	122	H	H
2	122	R	R
1	123	H	H
2	123	S	S
1	124	H	H
2	124	T	T
1	125	I	I
2	125	J	J
1	126	I	I
2	126	K	K
1	127	I	I
2	127	L	L
1	128	I	I
2	128	M	M
1	129	I	I
2	129	N	N
1	130	I	I
2	130	O	O
1	131	I	I
2	131	P	P
1	132	I	I
2	132	Q	Q
1	133	I	I
2	133	R	R
1	134	I	I
2	134	S	S
1	135	I	I
2	135	T	T
1	136	J	J
2	136	K	K
1	137	J	J
2	137	L	L
1	138	J	J
2	138	M	M
1	139	J	J
2	139	N	N
1	140	J	J
2	140	O	O
1	141	J	J
2	141	P	P
1	142	J	J
2	142	Q	Q
1	143	J	J
2	143	R	R
1	144	J	J
2	144	S	S
1	145	J	J
2	145	T	T
1	146	K	K
2	146	L	L
1	147	K	K
2	147	M	M
1	148	K	K
2	148	N	N
1	149	K	K
2	149	O	O
1	150	K	K
2	150	P	P
1	151	K	K
2	151	Q	Q
1	152	K	K
2	152	R	R
1	153	K	K
2	153	S	S
1	154	K	K
2	154	T	T
1	155	L	L
2	155	M	M
1	156	L	L
2	156	N	N
1	157	L	L
2	157	O	O
1	158	L	L
2	158	P	P
1	159	L	L
2	159	Q	Q
1	160	L	L
2	160	R	R
1	161	L	L
2	161	S	S
1	162	L	L
2	162	T	T
1	163	M	M
2	163	N	N
1	164	M	M
2	164	O	O
1	165	M	M
2	165	P	P
1	166	M	M
2	166	Q	Q
1	167	M	M
2	167	R	R
1	168	M	M
2	168	S	S
1	169	M	M
2	169	T	T
1	170	N	N
2	170	O	O
1	171	N	N
2	171	P	P
1	172	N	N
2	172	Q	Q
1	173	N	N
2	173	R	R
1	174	N	N
2	174	S	S
1	175	N	N
2	175	T	T
1	176	O	O
2	176	P	P
1	177	O	O
2	177	Q	Q
1	178	O	O
2	178	R	R
1	179	O	O
2	179	S	S
1	180	O	O
2	180	T	T
1	181	P	P
2	181	Q	Q
1	182	P	P
2	182	R	R
1	183	P	P
2	183	S	S
1	184	P	P
2	184	T	T
1	185	Q	Q
2	185	R	R
1	186	Q	Q
2	186	S	S
1	187	Q	Q
2	187	T	T
1	188	R	R
2	188	S	S
1	189	R	R
2	189	T	T
1	190	S	S
2	190	T	T

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190

Components

#1: Protein

A B C D E F G H I J K L M N O P Q R S T
Fructose-6-phosphate aldolase 1 / Fructose-6-phosphate aldolase A / FSAA

Details:

Mass: 23845.637 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0825, fsa, fsaA, JW5109, mipB, ybiZ / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P78055, Lyases; Carbon-carbon lyases; Aldehyde-lyases

#2: Chemical

B-301 G-301 H-301 K-301 P-301
ChemComp-P2D / pentane-2,4-dione

Details:

Mass: 100.116 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₅H₈O₂

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H₂O

• Has protein modification: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.45 ų/Da / Density % sol: 49.7 %
• Crystal grow: Temperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 8.5 ; Details: 25% PEG3350, 0.1M Tris-HCl pH 8.5, 0.2M LiCl , VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
• Radiation: Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.91841 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.75
1	1	h,-k,-l	2	0.25

• Reflection: Resolution: 2.242→48.4 Å / Num. all: 232071 / Num. obs: 232071 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 16.8
• Reflection shell: Resolution: 2.242→2.29 Å / R_merge(I) obs: 0.603 / Mean I/σ(I) obs: 2.6 / Num. unique all: 10244 / % possible all: 95.6

Processing

Software

Name	Version	Classification
ProDC		data collection
PHASER		phasing
REFMAC	5.8.0073	refinement
XDS		data reduction
Aimless		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RXF

4rxf

Resolution: 2.242→48.39 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.895 / SU B: 5.598 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.076 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.25101	10991	5.1 %	RANDOM
Rwork	0.23229	-	-	-
all	0.23324	205760	-	-
obs	0.23324	205760	98.74 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 43.374 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	10.37 Å2	0 Å2	3.89 Å2
2-	-	9.36 Å2	0 Å2
3-	-	-	-19.73 Å2

Refinement step

Cycle: LAST / Resolution: 2.242→48.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	32300	0	30	745	33075

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	32850
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	32985
X-RAY DIFFRACTION	r_angle_refined_deg	1.142	1.983	44720
X-RAY DIFFRACTION	r_angle_other_deg	1.062	3	75790
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.335	5	4380
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.922	25.179	1120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.006	15	5440
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.472	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	5460
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	37240
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	6640
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.196	4.243	17580
X-RAY DIFFRACTION	r_mcbond_other	3.196	4.243	17579
X-RAY DIFFRACTION	r_mcangle_it	4.65	6.355	21940
X-RAY DIFFRACTION	r_mcangle_other	4.65	6.355	21941
X-RAY DIFFRACTION	r_scbond_it	2.978	4.457	15268
X-RAY DIFFRACTION	r_scbond_other	2.978	4.457	15268
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.48	6.568	22779
X-RAY DIFFRACTION	r_long_range_B_refined	6.848	33.11	35459
X-RAY DIFFRACTION	r_long_range_B_other	6.824	33.118	35352
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	13469	0.04
1	2	B	13469	0.04
2	1	A	13490	0.03
2	2	C	13490	0.03
3	1	A	13427	0.04
3	2	D	13427	0.04
4	1	A	13653	0.02
4	2	E	13653	0.02
5	1	A	13497	0.03
5	2	F	13497	0.03
6	1	A	13571	0.03
6	2	G	13571	0.03
7	1	A	13549	0.03
7	2	H	13549	0.03
8	1	A	13569	0.03
8	2	I	13569	0.03
9	1	A	13598	0.03
9	2	J	13598	0.03
10	1	A	13481	0.03
10	2	K	13481	0.03
11	1	A	13501	0.03
11	2	L	13501	0.03
12	1	A	13533	0.03
12	2	M	13533	0.03
13	1	A	13467	0.03
13	2	N	13467	0.03
14	1	A	13502	0.03
14	2	O	13502	0.03
15	1	A	13502	0.03
15	2	P	13502	0.03
16	1	A	13514	0.03
16	2	Q	13514	0.03
17	1	A	13535	0.02
17	2	R	13535	0.02
18	1	A	13530	0.03
18	2	S	13530	0.03
19	1	A	13515	0.03
19	2	T	13515	0.03
20	1	B	13524	0.04
20	2	C	13524	0.04
21	1	B	13517	0.04
21	2	D	13517	0.04
22	1	B	13496	0.04
22	2	E	13496	0.04
23	1	B	13519	0.04
23	2	F	13519	0.04
24	1	B	13449	0.04
24	2	G	13449	0.04
25	1	B	13507	0.04
25	2	H	13507	0.04
26	1	B	13447	0.04
26	2	I	13447	0.04
27	1	B	13577	0.03
27	2	J	13577	0.03
28	1	B	13543	0.04
28	2	K	13543	0.04
29	1	B	13454	0.04
29	2	L	13454	0.04
30	1	B	13564	0.04
30	2	M	13564	0.04
31	1	B	13419	0.05
31	2	N	13419	0.05
32	1	B	13533	0.04
32	2	O	13533	0.04
33	1	B	13483	0.04
33	2	P	13483	0.04
34	1	B	13541	0.04
34	2	Q	13541	0.04
35	1	B	13484	0.04
35	2	R	13484	0.04
36	1	B	13459	0.04
36	2	S	13459	0.04
37	1	B	13545	0.04
37	2	T	13545	0.04
38	1	C	13620	0.03
38	2	D	13620	0.03
39	1	C	13517	0.03
39	2	E	13517	0.03
40	1	C	13688	0
40	2	F	13688	0
41	1	C	13545	0.03
41	2	G	13545	0.03
42	1	C	13530	0.02
42	2	H	13530	0.02
43	1	C	13580	0.03
43	2	I	13580	0.03
44	1	C	13537	0.03
44	2	J	13537	0.03
45	1	C	13640	0.01
45	2	K	13640	0.01
46	1	C	13617	0.02
46	2	L	13617	0.02
47	1	C	13587	0.02
47	2	M	13587	0.02
48	1	C	13550	0.03
48	2	N	13550	0.03
49	1	C	13662	0.02
49	2	O	13662	0.02
50	1	C	13616	0.02
50	2	P	13616	0.02
51	1	C	13670	0.01
51	2	Q	13670	0.01
52	1	C	13651	0.02
52	2	R	13651	0.02
53	1	C	13622	0.02
53	2	S	13622	0.02
54	1	C	13673	0.01
54	2	T	13673	0.01
55	1	D	13456	0.04
55	2	E	13456	0.04
56	1	D	13623	0.03
56	2	F	13623	0.03
57	1	D	13485	0.04
57	2	G	13485	0.04
58	1	D	13519	0.03
58	2	H	13519	0.03
59	1	D	13514	0.04
59	2	I	13514	0.04
60	1	D	13537	0.03
60	2	J	13537	0.03
61	1	D	13572	0.03
61	2	K	13572	0.03
62	1	D	13549	0.04
62	2	L	13549	0.04
63	1	D	13519	0.03
63	2	M	13519	0.03
64	1	D	13482	0.04
64	2	N	13482	0.04
65	1	D	13593	0.03
65	2	O	13593	0.03
66	1	D	13551	0.03
66	2	P	13551	0.03
67	1	D	13606	0.03
67	2	Q	13606	0.03
68	1	D	13588	0.03
68	2	R	13588	0.03
69	1	D	13557	0.03
69	2	S	13557	0.03
70	1	D	13610	0.03
70	2	T	13610	0.03
71	1	E	13521	0.03
71	2	F	13521	0.03
72	1	E	13596	0.02
72	2	G	13596	0.02
73	1	E	13578	0.03
73	2	H	13578	0.03
74	1	E	13593	0.03
74	2	I	13593	0.03
75	1	E	13617	0.03
75	2	J	13617	0.03
76	1	E	13507	0.03
76	2	K	13507	0.03
77	1	E	13527	0.02
77	2	L	13527	0.02
78	1	E	13562	0.03
78	2	M	13562	0.03
79	1	E	13494	0.03
79	2	N	13494	0.03
80	1	E	13529	0.03
80	2	O	13529	0.03
81	1	E	13529	0.02
81	2	P	13529	0.02
82	1	E	13539	0.02
82	2	Q	13539	0.02
83	1	E	13566	0.02
83	2	R	13566	0.02
84	1	E	13559	0.03
84	2	S	13559	0.03
85	1	E	13541	0.02
85	2	T	13541	0.02
86	1	F	13545	0.03
86	2	G	13545	0.03
87	1	F	13532	0.02
87	2	H	13532	0.02
88	1	F	13577	0.03
88	2	I	13577	0.03
89	1	F	13542	0.03
89	2	J	13542	0.03
90	1	F	13638	0.01
90	2	K	13638	0.01
91	1	F	13617	0.02
91	2	L	13617	0.02
92	1	F	13588	0.02
92	2	M	13588	0.02
93	1	F	13550	0.03
93	2	N	13550	0.03
94	1	F	13660	0.02
94	2	O	13660	0.02
95	1	F	13619	0.02
95	2	P	13619	0.02
96	1	F	13671	0.01
96	2	Q	13671	0.01
97	1	F	13654	0.02
97	2	R	13654	0.02
98	1	F	13621	0.02
98	2	S	13621	0.02
99	1	F	13674	0.01
99	2	T	13674	0.01
100	1	G	13528	0.03
100	2	H	13528	0.03
101	1	G	13623	0.03
101	2	I	13623	0.03
102	1	G	13538	0.03
102	2	J	13538	0.03
103	1	G	13569	0.03
103	2	K	13569	0.03
104	1	G	13554	0.03
104	2	L	13554	0.03
105	1	G	13481	0.03
105	2	M	13481	0.03
106	1	G	13522	0.03
106	2	N	13522	0.03
107	1	G	13555	0.03
107	2	O	13555	0.03
108	1	G	13589	0.02
108	2	P	13589	0.02
109	1	G	13564	0.03
109	2	Q	13564	0.03
110	1	G	13587	0.02
110	2	R	13587	0.02
111	1	G	13586	0.03
111	2	S	13586	0.03
112	1	G	13567	0.03
112	2	T	13567	0.03
113	1	H	13526	0.03
113	2	I	13526	0.03
114	1	H	13593	0.03
114	2	J	13593	0.03
115	1	H	13521	0.02
115	2	K	13521	0.02
116	1	H	13461	0.03
116	2	L	13461	0.03
117	1	H	13537	0.02
117	2	M	13537	0.02
118	1	H	13391	0.04
118	2	N	13391	0.04
119	1	H	13503	0.03
119	2	O	13503	0.03
120	1	H	13499	0.03
120	2	P	13499	0.03
121	1	H	13515	0.02
121	2	Q	13515	0.02
122	1	H	13498	0.03
122	2	R	13498	0.03
123	1	H	13570	0.02
123	2	S	13570	0.02
124	1	H	13518	0.02
124	2	T	13518	0.02
125	1	I	13533	0.04
125	2	J	13533	0.04
126	1	I	13532	0.03
126	2	K	13532	0.03
127	1	I	13587	0.02
127	2	L	13587	0.02
128	1	I	13481	0.03
128	2	M	13481	0.03
129	1	I	13519	0.04
129	2	N	13519	0.04
130	1	I	13555	0.03
130	2	O	13555	0.03
131	1	I	13590	0.02
131	2	P	13590	0.02
132	1	I	13561	0.03
132	2	Q	13561	0.03
133	1	I	13622	0.02
133	2	R	13622	0.02
134	1	I	13621	0.03
134	2	S	13621	0.03
135	1	I	13565	0.03
135	2	T	13565	0.03
136	1	J	13525	0.03
136	2	K	13525	0.03
137	1	J	13468	0.04
137	2	L	13468	0.04
138	1	J	13579	0.03
138	2	M	13579	0.03
139	1	J	13435	0.04
139	2	N	13435	0.04
140	1	J	13546	0.03
140	2	O	13546	0.03
141	1	J	13467	0.03
141	2	P	13467	0.03
142	1	J	13559	0.03
142	2	Q	13559	0.03
143	1	J	13502	0.03
143	2	R	13502	0.03
144	1	J	13576	0.03
144	2	S	13576	0.03
145	1	J	13562	0.03
145	2	T	13562	0.03
146	1	K	13569	0.02
146	2	L	13569	0.02
147	1	K	13575	0.02
147	2	M	13575	0.02
148	1	K	13535	0.03
148	2	N	13535	0.03
149	1	K	13651	0.02
149	2	O	13651	0.02
150	1	K	13609	0.02
150	2	P	13609	0.02
151	1	K	13658	0.01
151	2	Q	13658	0.01
152	1	K	13605	0.02
152	2	R	13605	0.02
153	1	K	13576	0.02
153	2	S	13576	0.02
154	1	K	13660	0.01
154	2	T	13660	0.01
155	1	L	13578	0.02
155	2	M	13578	0.02
156	1	L	13558	0.03
156	2	N	13558	0.03
157	1	L	13591	0.03
157	2	O	13591	0.03
158	1	L	13621	0.01
158	2	P	13621	0.01
159	1	L	13600	0.02
159	2	Q	13600	0.02
160	1	L	13660	0.01
160	2	R	13660	0.01
161	1	L	13553	0.03
161	2	S	13553	0.03
162	1	L	13603	0.02
162	2	T	13603	0.02
163	1	M	13485	0.03
163	2	N	13485	0.03
164	1	M	13598	0.02
164	2	O	13598	0.02
165	1	M	13515	0.03
165	2	P	13515	0.03
166	1	M	13605	0.02
166	2	Q	13605	0.02
167	1	M	13552	0.02
167	2	R	13552	0.02
168	1	M	13522	0.02
168	2	S	13522	0.02
169	1	M	13609	0.02
169	2	T	13609	0.02
170	1	N	13559	0.03
170	2	O	13559	0.03
171	1	N	13555	0.03
171	2	P	13555	0.03
172	1	N	13567	0.03
172	2	Q	13567	0.03
173	1	N	13591	0.03
173	2	R	13591	0.03
174	1	N	13481	0.04
174	2	S	13481	0.04
175	1	N	13572	0.03
175	2	T	13572	0.03
176	1	O	13588	0.03
176	2	P	13588	0.03
177	1	O	13680	0.01
177	2	Q	13680	0.01
178	1	O	13626	0.02
178	2	R	13626	0.02
179	1	O	13596	0.02
179	2	S	13596	0.02
180	1	O	13683	0.01
180	2	T	13683	0.01
181	1	P	13599	0.02
181	2	Q	13599	0.02
182	1	P	13659	0.01
182	2	R	13659	0.01
183	1	P	13549	0.02
183	2	S	13549	0.02
184	1	P	13602	0.02
184	2	T	13602	0.02
185	1	Q	13633	0.02
185	2	R	13633	0.02
186	1	Q	13606	0.02
186	2	S	13606	0.02
187	1	Q	13693	0
187	2	T	13693	0
188	1	R	13588	0.02
188	2	S	13588	0.02
189	1	R	13638	0.02
189	2	T	13638	0.02
190	1	S	13609	0.02
190	2	T	13609	0.02

LS refinement shell

Resolution: 2.242→2.3 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.326	726	-
Rwork	0.293	13069	-
obs	-	-	85.2 %