PDB-6ba1: Purine-Preferring Ribonucleoside Hydrolase from Gardnerella vaginalis

Basic information

• Entry: Database: PDB / ID: 6ba1
• Title: Purine-Preferring Ribonucleoside Hydrolase from Gardnerella vaginalis
• Components: Inosine-uridine preferring nucleoside hydrolase
• Keywords: HYDROLASE / Nucleoside Hydrolase Nitrogen Metabolism

Function / homology

Function:

purine nucleosidase / purine nucleosidase activity / metabolic process

Domain/homology:

Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta

Component:

Inosine-uridine preferring nucleoside hydrolase

• Biological species: Gardnerella vaginalis 315-A (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
• Authors: Renner, N. / Jacques, D.A.

Funding support

Australia, 1items

Organization	Grant number	Country
National Health and Medical Research Council (NHMRC, Australia)	GNT1036521	Australia

• Citation: Journal: To Be Published; Title: Inosine-Uridine Preferring Ribonucleoside Hydrolase from Gardnerella vaginalis; Authors: Renner, N. / Jacques, D.A.

History

Deposition	Oct 11, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Assembly

Deposited unit

A: Inosine-uridine preferring nucleoside hydrolase

B: Inosine-uridine preferring nucleoside hydrolase

C: Inosine-uridine preferring nucleoside hydrolase

D: Inosine-uridine preferring nucleoside hydrolase

E: Inosine-uridine preferring nucleoside hydrolase

F: Inosine-uridine preferring nucleoside hydrolase

G: Inosine-uridine preferring nucleoside hydrolase

H: Inosine-uridine preferring nucleoside hydrolase

I: Inosine-uridine preferring nucleoside hydrolase

J: Inosine-uridine preferring nucleoside hydrolase

K: Inosine-uridine preferring nucleoside hydrolase

L: Inosine-uridine preferring nucleoside hydrolase

M: Inosine-uridine preferring nucleoside hydrolase

N: Inosine-uridine preferring nucleoside hydrolase

O: Inosine-uridine preferring nucleoside hydrolase

P: Inosine-uridine preferring nucleoside hydrolase

Q: Inosine-uridine preferring nucleoside hydrolase

R: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• 621 kDa, 18 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	620,576	36
Polymers	619,855	18
Non-polymers	721	18
Water	0	0

1

A: Inosine-uridine preferring nucleoside hydrolase

E: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• Evidence: gel filtration
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2330 Å2
ΔGint	-39 kcal/mol
Surface area	22730 Å2
Method	PISA

2

B: Inosine-uridine preferring nucleoside hydrolase

D: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2350 Å2
ΔGint	-40 kcal/mol
Surface area	22840 Å2
Method	PISA

3

C: Inosine-uridine preferring nucleoside hydrolase

I: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2300 Å2
ΔGint	-39 kcal/mol
Surface area	22730 Å2
Method	PISA

4

F: Inosine-uridine preferring nucleoside hydrolase

H: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2400 Å2
ΔGint	-39 kcal/mol
Surface area	22610 Å2
Method	PISA

5

G: Inosine-uridine preferring nucleoside hydrolase

L: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2350 Å2
ΔGint	-39 kcal/mol
Surface area	22840 Å2
Method	PISA

6

J: Inosine-uridine preferring nucleoside hydrolase

P: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2390 Å2
ΔGint	-40 kcal/mol
Surface area	22660 Å2
Method	PISA

7

K: Inosine-uridine preferring nucleoside hydrolase

N: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2380 Å2
ΔGint	-39 kcal/mol
Surface area	22540 Å2
Method	PISA

8

M: Inosine-uridine preferring nucleoside hydrolase

R: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2360 Å2
ΔGint	-39 kcal/mol
Surface area	22560 Å2
Method	PISA

9

O: Inosine-uridine preferring nucleoside hydrolase

Q: Inosine-uridine preferring nucleoside hydrolase

hetero molecules

Summary:

• defined by author&software
• 69 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	68,953	4
Polymers	68,873	2
Non-polymers	80	2
Water	0

Symmetry operations:

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

Calculated values:

Buried area	2370 Å2
ΔGint	-39 kcal/mol
Surface area	22720 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	163.270, 80.240, 223.820
Angle α, β, γ (deg.)	90.000, 106.500, 90.000
Int Tables number	4
Space group name H-M	P1211

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	B
2	18	C
1	19	B
2	19	D
1	20	B
2	20	E
1	21	B
2	21	F
1	22	B
2	22	G
1	23	B
2	23	H
1	24	B
2	24	I
1	25	B
2	25	J
1	26	B
2	26	K
1	27	B
2	27	L
1	28	B
2	28	M
1	29	B
2	29	N
1	30	B
2	30	O
1	31	B
2	31	P
1	32	B
2	32	Q
1	33	B
2	33	R
1	34	C
2	34	D
1	35	C
2	35	E
1	36	C
2	36	F
1	37	C
2	37	G
1	38	C
2	38	H
1	39	C
2	39	I
1	40	C
2	40	J
1	41	C
2	41	K
1	42	C
2	42	L
1	43	C
2	43	M
1	44	C
2	44	N
1	45	C
2	45	O
1	46	C
2	46	P
1	47	C
2	47	Q
1	48	C
2	48	R
1	49	D
2	49	E
1	50	D
2	50	F
1	51	D
2	51	G
1	52	D
2	52	H
1	53	D
2	53	I
1	54	D
2	54	J
1	55	D
2	55	K
1	56	D
2	56	L
1	57	D
2	57	M
1	58	D
2	58	N
1	59	D
2	59	O
1	60	D
2	60	P
1	61	D
2	61	Q
1	62	D
2	62	R
1	63	E
2	63	F
1	64	E
2	64	G
1	65	E
2	65	H
1	66	E
2	66	I
1	67	E
2	67	J
1	68	E
2	68	K
1	69	E
2	69	L
1	70	E
2	70	M
1	71	E
2	71	N
1	72	E
2	72	O
1	73	E
2	73	P
1	74	E
2	74	Q
1	75	E
2	75	R
1	76	F
2	76	G
1	77	F
2	77	H
1	78	F
2	78	I
1	79	F
2	79	J
1	80	F
2	80	K
1	81	F
2	81	L
1	82	F
2	82	M
1	83	F
2	83	N
1	84	F
2	84	O
1	85	F
2	85	P
1	86	F
2	86	Q
1	87	F
2	87	R
1	88	G
2	88	H
1	89	G
2	89	I
1	90	G
2	90	J
1	91	G
2	91	K
1	92	G
2	92	L
1	93	G
2	93	M
1	94	G
2	94	N
1	95	G
2	95	O
1	96	G
2	96	P
1	97	G
2	97	Q
1	98	G
2	98	R
1	99	H
2	99	I
1	100	H
2	100	J
1	101	H
2	101	K
1	102	H
2	102	L
1	103	H
2	103	M
1	104	H
2	104	N
1	105	H
2	105	O
1	106	H
2	106	P
1	107	H
2	107	Q
1	108	H
2	108	R
1	109	I
2	109	J
1	110	I
2	110	K
1	111	I
2	111	L
1	112	I
2	112	M
1	113	I
2	113	N
1	114	I
2	114	O
1	115	I
2	115	P
1	116	I
2	116	Q
1	117	I
2	117	R
1	118	J
2	118	K
1	119	J
2	119	L
1	120	J
2	120	M
1	121	J
2	121	N
1	122	J
2	122	O
1	123	J
2	123	P
1	124	J
2	124	Q
1	125	J
2	125	R
1	126	K
2	126	L
1	127	K
2	127	M
1	128	K
2	128	N
1	129	K
2	129	O
1	130	K
2	130	P
1	131	K
2	131	Q
1	132	K
2	132	R
1	133	L
2	133	M
1	134	L
2	134	N
1	135	L
2	135	O
1	136	L
2	136	P
1	137	L
2	137	Q
1	138	L
2	138	R
1	139	M
2	139	N
1	140	M
2	140	O
1	141	M
2	141	P
1	142	M
2	142	Q
1	143	M
2	143	R
1	144	N
2	144	O
1	145	N
2	145	P
1	146	N
2	146	Q
1	147	N
2	147	R
1	148	O
2	148	P
1	149	O
2	149	Q
1	150	O
2	150	R
1	151	P
2	151	Q
1	152	P
2	152	R
1	153	Q
2	153	R

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 317 / Label seq-ID: 5 - 320

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	B	B
2	18	C	C
1	19	B	B
2	19	D	D
1	20	B	B
2	20	E	E
1	21	B	B
2	21	F	F
1	22	B	B
2	22	G	G
1	23	B	B
2	23	H	H
1	24	B	B
2	24	I	I
1	25	B	B
2	25	J	J
1	26	B	B
2	26	K	K
1	27	B	B
2	27	L	L
1	28	B	B
2	28	M	M
1	29	B	B
2	29	N	N
1	30	B	B
2	30	O	O
1	31	B	B
2	31	P	P
1	32	B	B
2	32	Q	Q
1	33	B	B
2	33	R	R
1	34	C	C
2	34	D	D
1	35	C	C
2	35	E	E
1	36	C	C
2	36	F	F
1	37	C	C
2	37	G	G
1	38	C	C
2	38	H	H
1	39	C	C
2	39	I	I
1	40	C	C
2	40	J	J
1	41	C	C
2	41	K	K
1	42	C	C
2	42	L	L
1	43	C	C
2	43	M	M
1	44	C	C
2	44	N	N
1	45	C	C
2	45	O	O
1	46	C	C
2	46	P	P
1	47	C	C
2	47	Q	Q
1	48	C	C
2	48	R	R
1	49	D	D
2	49	E	E
1	50	D	D
2	50	F	F
1	51	D	D
2	51	G	G
1	52	D	D
2	52	H	H
1	53	D	D
2	53	I	I
1	54	D	D
2	54	J	J
1	55	D	D
2	55	K	K
1	56	D	D
2	56	L	L
1	57	D	D
2	57	M	M
1	58	D	D
2	58	N	N
1	59	D	D
2	59	O	O
1	60	D	D
2	60	P	P
1	61	D	D
2	61	Q	Q
1	62	D	D
2	62	R	R
1	63	E	E
2	63	F	F
1	64	E	E
2	64	G	G
1	65	E	E
2	65	H	H
1	66	E	E
2	66	I	I
1	67	E	E
2	67	J	J
1	68	E	E
2	68	K	K
1	69	E	E
2	69	L	L
1	70	E	E
2	70	M	M
1	71	E	E
2	71	N	N
1	72	E	E
2	72	O	O
1	73	E	E
2	73	P	P
1	74	E	E
2	74	Q	Q
1	75	E	E
2	75	R	R
1	76	F	F
2	76	G	G
1	77	F	F
2	77	H	H
1	78	F	F
2	78	I	I
1	79	F	F
2	79	J	J
1	80	F	F
2	80	K	K
1	81	F	F
2	81	L	L
1	82	F	F
2	82	M	M
1	83	F	F
2	83	N	N
1	84	F	F
2	84	O	O
1	85	F	F
2	85	P	P
1	86	F	F
2	86	Q	Q
1	87	F	F
2	87	R	R
1	88	G	G
2	88	H	H
1	89	G	G
2	89	I	I
1	90	G	G
2	90	J	J
1	91	G	G
2	91	K	K
1	92	G	G
2	92	L	L
1	93	G	G
2	93	M	M
1	94	G	G
2	94	N	N
1	95	G	G
2	95	O	O
1	96	G	G
2	96	P	P
1	97	G	G
2	97	Q	Q
1	98	G	G
2	98	R	R
1	99	H	H
2	99	I	I
1	100	H	H
2	100	J	J
1	101	H	H
2	101	K	K
1	102	H	H
2	102	L	L
1	103	H	H
2	103	M	M
1	104	H	H
2	104	N	N
1	105	H	H
2	105	O	O
1	106	H	H
2	106	P	P
1	107	H	H
2	107	Q	Q
1	108	H	H
2	108	R	R
1	109	I	I
2	109	J	J
1	110	I	I
2	110	K	K
1	111	I	I
2	111	L	L
1	112	I	I
2	112	M	M
1	113	I	I
2	113	N	N
1	114	I	I
2	114	O	O
1	115	I	I
2	115	P	P
1	116	I	I
2	116	Q	Q
1	117	I	I
2	117	R	R
1	118	J	J
2	118	K	K
1	119	J	J
2	119	L	L
1	120	J	J
2	120	M	M
1	121	J	J
2	121	N	N
1	122	J	J
2	122	O	O
1	123	J	J
2	123	P	P
1	124	J	J
2	124	Q	Q
1	125	J	J
2	125	R	R
1	126	K	K
2	126	L	L
1	127	K	K
2	127	M	M
1	128	K	K
2	128	N	N
1	129	K	K
2	129	O	O
1	130	K	K
2	130	P	P
1	131	K	K
2	131	Q	Q
1	132	K	K
2	132	R	R
1	133	L	L
2	133	M	M
1	134	L	L
2	134	N	N
1	135	L	L
2	135	O	O
1	136	L	L
2	136	P	P
1	137	L	L
2	137	Q	Q
1	138	L	L
2	138	R	R
1	139	M	M
2	139	N	N
1	140	M	M
2	140	O	O
1	141	M	M
2	141	P	P
1	142	M	M
2	142	Q	Q
1	143	M	M
2	143	R	R
1	144	N	N
2	144	O	O
1	145	N	N
2	145	P	P
1	146	N	N
2	146	Q	Q
1	147	N	N
2	147	R	R
1	148	O	O
2	148	P	P
1	149	O	O
2	149	Q	Q
1	150	O	O
2	150	R	R
1	151	P	P
2	151	Q	Q
1	152	P	P
2	152	R	R
1	153	Q	Q
2	153	R	R

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

Components

#1: Protein

A B C D E F G H I J K L M N O P Q R
Inosine-uridine preferring nucleoside hydrolase

Details:

Mass: 34436.387 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gardnerella vaginalis 315-A (bacteria) / Gene: HMPREF9435_1145 / Plasmid: pOPTG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F5LUS2, purine nucleosidase

#2: Chemical

A-400 B-400 C-400 D-400 E-400 F-400 G-400 H-400 I-400 J-400 K-400 L-400 M-400 N-400 O-400 P-400 Q-400 R-400
ChemComp-CA / CALCIUM ION

Details:

Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.27 ų/Da / Density % sol: 45.76 %
• Crystal grow: Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 ; Details: 23% (w/v) PEG 4000 0.2M Magnesium Chloride 0.05M TRIS

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
• Detector: Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 14, 2017
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9537 Å / Relative weight: 1
• Reflection: Resolution: 2.9→80.24 Å / Num. obs: 122214 / % possible obs: 98.6 % / Redundancy: 6.8 %; Data reduction details: The data were highly anisotropic accounting for the high Rmerge value generated in AIMLESS. The data were subsequently ellipsoidally truncated and anisotropically scaled using the anisotropy server to improve the maps. The discrepency between reflections used in refinement and those in data collection are the result of ellipsoidal truncation of the data.; CC_1/2: 0.995 / R_merge(I) obs: 0.234 / R_pim(I) all: 0.095 / R_rim(I) all: 0.253 / Net I/σ(I): 7.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	% possible all
2.9-2.95	6	2.797	5841	0.641	1.189	3.048	96.2
15.88-80.24	5.9	0.051	823	0.997	0.023	0.056	98.1

Phasing

• Phasing: Method: molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	5.31 Å	78.27 Å
Translation	5.31 Å	78.27 Å

Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
Aimless	0.5.32	data scaling
PHASER	2.7.17	phasing
PDB_EXTRACT	3.22	data extraction
MOSFLM	7.2.1	data reduction
Blu-Ice		data collection

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPO

4kpo

Resolution: 2.9→80.24 Å / Cor.coef. F_o:F_c: 0.804 / Cor.coef. F_o:F_c free: 0.808 / SU B: 68.913 / SU ML: 0.52 / SU R Cruickshank DPI: 0.6118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.622
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2816	4795	5 %	RANDOM
Rwork	0.2788	-	-	-
obs	0.2789	90434	76.98 %	-

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

Displacement parameters

B_iso max: 154.3 Ų / B_iso mean: 43.388 Ų / B_iso min: 19.81 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	4.53 Å2	0 Å2	1.85 Å2
2-	-	-3.89 Å2	0 Å2
3-	-	-	-1.48 Å2

Refinement step

Cycle: final / Resolution: 2.9→80.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42451	0	18	0	42469
Biso mean	-	-	33.29	-	-
Num. residues	-	-	-	-	5688

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	43207
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	40976
X-RAY DIFFRACTION	r_angle_refined_deg	1.266	1.98	58928
X-RAY DIFFRACTION	r_angle_other_deg	0.915	3	95030
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.399	5	5670
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.06	25.465	1645
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.367	15	7054
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13	15	157
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	7128
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	48173
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	7720

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	20302	0.02
1	2	B	20302	0.02
2	1	A	20368	0.01
2	2	C	20368	0.01
3	1	A	20306	0.02
3	2	D	20306	0.02
4	1	A	20238	0.02
4	2	E	20238	0.02
5	1	A	20128	0.03
5	2	F	20128	0.03
6	1	A	20202	0.03
6	2	G	20202	0.03
7	1	A	20214	0.03
7	2	H	20214	0.03
8	1	A	20266	0.02
8	2	I	20266	0.02
9	1	A	20164	0.02
9	2	J	20164	0.02
10	1	A	20226	0.02
10	2	K	20226	0.02
11	1	A	20198	0.03
11	2	L	20198	0.03
12	1	A	20218	0.03
12	2	M	20218	0.03
13	1	A	20180	0.02
13	2	N	20180	0.02
14	1	A	20318	0.02
14	2	O	20318	0.02
15	1	A	20254	0.02
15	2	P	20254	0.02
16	1	A	20118	0.02
16	2	Q	20118	0.02
17	1	A	20082	0.03
17	2	R	20082	0.03
18	1	B	20340	0.02
18	2	C	20340	0.02
19	1	B	20324	0.02
19	2	D	20324	0.02
20	1	B	20268	0.01
20	2	E	20268	0.01
21	1	B	20200	0.02
21	2	F	20200	0.02
22	1	B	20264	0.02
22	2	G	20264	0.02
23	1	B	20236	0.02
23	2	H	20236	0.02
24	1	B	20276	0.01
24	2	I	20276	0.01
25	1	B	20230	0
25	2	J	20230	0
26	1	B	20282	0.01
26	2	K	20282	0.01
27	1	B	20262	0.02
27	2	L	20262	0.02
28	1	B	20220	0.02
28	2	M	20220	0.02
29	1	B	20244	0
29	2	N	20244	0
30	1	B	20334	0.01
30	2	O	20334	0.01
31	1	B	20324	0.01
31	2	P	20324	0.01
32	1	B	20196	0.02
32	2	Q	20196	0.02
33	1	B	20166	0.02
33	2	R	20166	0.02
34	1	C	20334	0.02
34	2	D	20334	0.02
35	1	C	20252	0.02
35	2	E	20252	0.02
36	1	C	20154	0.02
36	2	F	20154	0.02
37	1	C	20220	0.02
37	2	G	20220	0.02
38	1	C	20248	0.03
38	2	H	20248	0.03
39	1	C	20282	0.02
39	2	I	20282	0.02
40	1	C	20184	0.01
40	2	J	20184	0.01
41	1	C	20238	0.02
41	2	K	20238	0.02
42	1	C	20212	0.02
42	2	L	20212	0.02
43	1	C	20238	0.02
43	2	M	20238	0.02
44	1	C	20200	0.01
44	2	N	20200	0.01
45	1	C	20352	0.01
45	2	O	20352	0.01
46	1	C	20278	0.02
46	2	P	20278	0.02
47	1	C	20142	0.02
47	2	Q	20142	0.02
48	1	C	20110	0.02
48	2	R	20110	0.02
49	1	D	20294	0.02
49	2	E	20294	0.02
50	1	D	20238	0.02
50	2	F	20238	0.02
51	1	D	20242	0.01
51	2	G	20242	0.01
52	1	D	20318	0.02
52	2	H	20318	0.02
53	1	D	20332	0.02
53	2	I	20332	0.02
54	1	D	20238	0
54	2	J	20238	0
55	1	D	20298	0.01
55	2	K	20298	0.01
56	1	D	20286	0.02
56	2	L	20286	0.02
57	1	D	20266	0.02
57	2	M	20266	0.02
58	1	D	20244	0.01
58	2	N	20244	0.01
59	1	D	20360	0.01
59	2	O	20360	0.01
60	1	D	20282	0.02
60	2	P	20282	0.02
61	1	D	20184	0.02
61	2	Q	20184	0.02
62	1	D	20170	0.02
62	2	R	20170	0.02
63	1	E	20198	0.02
63	2	F	20198	0.02
64	1	E	20254	0.02
64	2	G	20254	0.02
65	1	E	20226	0.02
65	2	H	20226	0.02
66	1	E	20250	0.02
66	2	I	20250	0.02
67	1	E	20182	0.01
67	2	J	20182	0.01
68	1	E	20224	0.02
68	2	K	20224	0.02
69	1	E	20264	0.02
69	2	L	20264	0.02
70	1	E	20188	0.02
70	2	M	20188	0.02
71	1	E	20174	0.01
71	2	N	20174	0.01
72	1	E	20278	0.01
72	2	O	20278	0.01
73	1	E	20224	0.02
73	2	P	20224	0.02
74	1	E	20196	0.02
74	2	Q	20196	0.02
75	1	E	20152	0.02
75	2	R	20152	0.02
76	1	F	20218	0.01
76	2	G	20218	0.01
77	1	F	20168	0.03
77	2	H	20168	0.03
78	1	F	20210	0.01
78	2	I	20210	0.01
79	1	F	20158	0.01
79	2	J	20158	0.01
80	1	F	20234	0
80	2	K	20234	0
81	1	F	20242	0.01
81	2	L	20242	0.01
82	1	F	20144	0.01
82	2	M	20144	0.01
83	1	F	20152	0.01
83	2	N	20152	0.01
84	1	F	20194	0.02
84	2	O	20194	0.02
85	1	F	20200	0.01
85	2	P	20200	0.01
86	1	F	20160	0.01
86	2	Q	20160	0.01
87	1	F	20190	0.02
87	2	R	20190	0.02
88	1	G	20164	0.02
88	2	H	20164	0.02
89	1	G	20232	0.01
89	2	I	20232	0.01
90	1	G	20172	0.01
90	2	J	20172	0.01
91	1	G	20248	0
91	2	K	20248	0
92	1	G	20278	0.01
92	2	L	20278	0.01
93	1	G	20182	0.01
93	2	M	20182	0.01
94	1	G	20170	0.01
94	2	N	20170	0.01
95	1	G	20246	0.01
95	2	O	20246	0.01
96	1	G	20252	0.01
96	2	P	20252	0.01
97	1	G	20210	0.01
97	2	Q	20210	0.01
98	1	G	20166	0.01
98	2	R	20166	0.01
99	1	H	20286	0.03
99	2	I	20286	0.03
100	1	H	20184	0.02
100	2	J	20184	0.02
101	1	H	20238	0.02
101	2	K	20238	0.02
102	1	H	20186	0.02
102	2	L	20186	0.02
103	1	H	20198	0.03
103	2	M	20198	0.03
104	1	H	20198	0.02
104	2	N	20198	0.02
105	1	H	20288	0.02
105	2	O	20288	0.02
106	1	H	20220	0.02
106	2	P	20220	0.02
107	1	H	20104	0.02
107	2	Q	20104	0.02
108	1	H	20108	0.02
108	2	R	20108	0.02
109	1	I	20208	0.01
109	2	J	20208	0.01
110	1	I	20290	0.01
110	2	K	20290	0.01
111	1	I	20242	0.01
111	2	L	20242	0.01
112	1	I	20270	0.01
112	2	M	20270	0.01
113	1	I	20234	0.01
113	2	N	20234	0.01
114	1	I	20320	0.01
114	2	O	20320	0.01
115	1	I	20276	0.01
115	2	P	20276	0.01
116	1	I	20162	0.01
116	2	Q	20162	0.01
117	1	I	20156	0.01
117	2	R	20156	0.01
118	1	J	20240	0.01
118	2	K	20240	0.01
119	1	J	20176	0.01
119	2	L	20176	0.01
120	1	J	20190	0.01
120	2	M	20190	0.01
121	1	J	20240	0
121	2	N	20240	0
122	1	J	20222	0
122	2	O	20222	0
123	1	J	20212	0.01
123	2	P	20212	0.01
124	1	J	20180	0.01
124	2	Q	20180	0.01
125	1	J	20160	0.01
125	2	R	20160	0.01
126	1	K	20254	0
126	2	L	20254	0
127	1	K	20222	0.01
127	2	M	20222	0.01
128	1	K	20230	0.01
128	2	N	20230	0.01
129	1	K	20280	0.01
129	2	O	20280	0.01
130	1	K	20292	0
130	2	P	20292	0
131	1	K	20188	0
131	2	Q	20188	0
132	1	K	20180	0
132	2	R	20180	0
133	1	L	20178	0.01
133	2	M	20178	0.01
134	1	L	20194	0.01
134	2	N	20194	0.01
135	1	L	20238	0.01
135	2	O	20238	0.01
136	1	L	20252	0.01
136	2	P	20252	0.01
137	1	L	20212	0.01
137	2	Q	20212	0.01
138	1	L	20178	0.01
138	2	R	20178	0.01
139	1	M	20230	0.01
139	2	N	20230	0.01
140	1	M	20272	0.01
140	2	O	20272	0.01
141	1	M	20210	0.01
141	2	P	20210	0.01
142	1	M	20182	0.01
142	2	Q	20182	0.01
143	1	M	20150	0.01
143	2	R	20150	0.01
144	1	N	20234	0.01
144	2	O	20234	0.01
145	1	N	20224	0.01
145	2	P	20224	0.01
146	1	N	20176	0.01
146	2	Q	20176	0.01
147	1	N	20160	0.01
147	2	R	20160	0.01
148	1	O	20290	0.02
148	2	P	20290	0.02
149	1	O	20168	0.01
149	2	Q	20168	0.01
150	1	O	20152	0.02
150	2	R	20152	0.02
151	1	P	20178	0.01
151	2	Q	20178	0.01
152	1	P	20154	0
152	2	R	20154	0
153	1	Q	20174	0.01
153	2	R	20174	0.01

LS refinement shell

Resolution: 2.902→2.978 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.272	26	-
Rwork	0.294	418	-
all	-	444	-
obs	-	-	4.86 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°2)	L12 (°2)	L13 (°2)	L22 (°2)	L23 (°2)	L33 (°2)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å2)	T12 (Å2)	T13 (Å2)	T22 (Å2)	T23 (Å2)	T33 (Å2)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.714	-0.2744	-0.3477	1.465	0.6022	1.753	-0.0422	0.1631	-0.0213	0.0329	-0.0678	0.0543	0.0156	-0.1077	0.1099	0.0232	-0.008	-0.0639	0.4922	-0.0562	0.2093	-15.33	-12.905	894.28
2	4.7508	-0.059	1.58	1.0832	0.016	1.085	-0.1828	0.1674	-0.3555	0.1405	0.333	0.0039	-0.3118	0.1531	-0.1502	0.1509	-0.0398	-0.0071	0.5233	-0.0546	0.2803	-59.867	-6.745	887.682
3	3.0873	-0.2035	1.7678	1.6882	-0.1758	1.1269	0.0294	-0.0825	0.0619	-0.0763	-0.0791	-0.2643	0.0631	0.0204	0.0497	0.0415	0.0487	-0.0556	0.5503	-0.045	0.2724	-63.144	-2.826	836.142
4	3.9573	-0.1404	1.3393	1.3569	0.7899	2.135	-0.0804	0.3262	0.0508	-0.0424	0.1056	0.0826	-0.416	-0.1094	-0.0252	0.131	0.0193	-0.0259	0.6097	0.1069	0.2363	-99.241	-3.438	872.53
5	3.251	0.356	0.4661	1.036	0.8248	0.9797	-0.0914	-0.1788	0.1954	-0.0886	0.055	-0.1585	-0.0351	0.0861	0.0364	0.0782	0.0654	-0.138	0.5343	-0.1326	0.5361	26.086	-9.555	902.587
6	4.34	0.1181	0.465	1.3263	0.7244	0.8683	-0.1047	0.1381	-0.0166	0.0647	0.1867	0.1693	0.1739	0.1297	-0.082	0.0856	0.076	-0.1149	0.6509	0.0527	0.3078	-19.515	-8.482	847.68
7	4.8931	0.8403	1.2167	0.7861	0.2513	1.9528	0.0079	-0.4338	0.0815	-0.205	-0.1562	0.0925	0.2669	-0.2021	0.1483	0.2955	-0.0267	-0.1355	0.4458	-0.0243	0.2737	-10.2	-17.398	937.423
8	4.4879	-0.747	0.3064	1.5598	0.0535	0.2071	0.0658	0.4779	-0.0012	-0.0327	-0.0739	0.0122	0.0595	0.2799	0.0081	0.1046	0.1422	-0.1489	0.8215	-0.0607	0.269	21.703	-8.104	856.439
9	2.6528	0.1365	1.0915	4.2134	-0.281	0.588	0.0704	-0.0967	-0.1327	-0.8281	0.0916	0.5983	0.0652	-0.012	-0.1619	0.2792	0.0321	-0.2758	0.453	-0.109	0.3963	-102.337	-5.532	820.076
10	6.2154	-0.0061	-0.542	0.9127	-0.9333	1.6533	0.251	0.1017	-0.0909	0.2026	-0.044	0.1571	-0.4991	-0.4031	-0.207	0.2233	0.1519	-0.0863	0.3954	0.0094	0.4529	-90.787	-16.628	966.561
11	4.4424	-0.3126	-0.1919	2.8587	-0.9813	0.9924	-0.3597	0.1471	-0.0901	0.4723	0.2981	-0.5077	0.0733	0.0173	0.0616	0.4189	0.0301	-0.4572	0.3656	-0.0584	0.5988	-45.859	-14.277	0.695
12	5.975	0.3056	2.0876	0.293	0.4771	1.877	-0.0899	0.0041	0.2674	-0.0175	-0.056	-0.124	0.2541	0.3634	0.146	0.1864	0.2057	0.0057	0.7756	0.1453	0.4231	30.278	-12.754	949.059
13	6.8326	1.0605	2.7852	2.0285	-0.6747	2.2604	0.1098	-0.2661	0.1634	0.209	-0.2768	0.0314	-0.1409	0.113	0.167	0.2097	-0.0105	-0.043	0.4593	-0.0654	0.3831	33.595	-11.22	997.672
14	3.6861	-0.2865	1.2054	1.1963	-0.0164	0.9147	0.1979	0.0434	-0.2024	0.2383	-0.0467	0.1124	0.2261	-0.4208	-0.1511	0.3668	-0.1703	-0.4079	0.4933	0.0846	0.6447	-86.887	-14.89	0.45
15	6.3195	-1.0311	1.5002	1.1177	-0.0801	1.1364	-0.0947	-0.4185	0.4981	-0.0554	-0.1087	0.0221	0.0566	-0.2511	0.2033	0.1047	0.0224	-0.0922	0.5615	-0.0649	0.3683	-95.225	-7.728	919.838
16	6.9031	-1.3231	-0.6664	1.1876	-0.1899	1.221	0.0597	-0.8441	-0.0116	-0.0534	0.0011	-0.2795	-0.1462	0.2312	-0.0608	0.1529	-0.0858	-0.1788	0.4299	0.0052	0.5597	-50.092	-22.434	975.368
17	6.0887	-1.4035	0.7532	0.4796	0.2369	1.3454	-0.2037	-0.5171	0.199	0.1596	0.1045	-0.0459	0.1311	-0.0071	0.0992	0.2076	-0.0298	-0.1017	0.661	-0.0342	0.4017	-55.272	-14.894	931.627
18	7.7968	0.4906	3.4679	0.7777	-0.2859	1.9128	0.0405	-0.7794	0.5038	-0.418	-0.1273	0.1094	0.3312	-0.3822	0.0868	0.2679	0.0169	-0.1897	0.4973	-0.2465	0.9599	-5.753	-15.988	983.356

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 317
2	X-RAY DIFFRACTION	1	A	400
3	X-RAY DIFFRACTION	2	B	2 - 317
4	X-RAY DIFFRACTION	2	B	400
5	X-RAY DIFFRACTION	3	C	2 - 317
6	X-RAY DIFFRACTION	3	C	400
7	X-RAY DIFFRACTION	4	D	2 - 317
8	X-RAY DIFFRACTION	4	D	400
9	X-RAY DIFFRACTION	5	E	2 - 317
10	X-RAY DIFFRACTION	5	E	400
11	X-RAY DIFFRACTION	6	F	2 - 317
12	X-RAY DIFFRACTION	6	F	400
13	X-RAY DIFFRACTION	7	G	2 - 317
14	X-RAY DIFFRACTION	7	G	400
15	X-RAY DIFFRACTION	8	H	2 - 317
16	X-RAY DIFFRACTION	8	H	400
17	X-RAY DIFFRACTION	9	I	2 - 317
18	X-RAY DIFFRACTION	9	I	400
19	X-RAY DIFFRACTION	10	J	2 - 317
20	X-RAY DIFFRACTION	10	J	400
21	X-RAY DIFFRACTION	11	K	2 - 317
22	X-RAY DIFFRACTION	11	K	400
23	X-RAY DIFFRACTION	12	L	2 - 317
24	X-RAY DIFFRACTION	12	L	400
25	X-RAY DIFFRACTION	13	M	2 - 317
26	X-RAY DIFFRACTION	13	M	400
27	X-RAY DIFFRACTION	14	N	2 - 317
28	X-RAY DIFFRACTION	14	N	400
29	X-RAY DIFFRACTION	15	O	2 - 317
30	X-RAY DIFFRACTION	15	O	400
31	X-RAY DIFFRACTION	16	P	2 - 317
32	X-RAY DIFFRACTION	16	P	400
33	X-RAY DIFFRACTION	17	Q	2 - 317
34	X-RAY DIFFRACTION	17	Q	400
35	X-RAY DIFFRACTION	18	R	2 - 317
36	X-RAY DIFFRACTION	18	R	400