PDB-4uv3: Structure of the curli transport lipoprotein CsgG in its membrane...

Basic information

• Entry: Database: PDB / ID: 4uv3
• Title: Structure of the curli transport lipoprotein CsgG in its membrane- bound conformation
• Components: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG
• Keywords: TRANSPORT PROTEIN / CSGG / CURLI TRANSPORTER / OUTER MEMBRANE LIPOPROTEIN / AMYLOID

Function / homology

Function:

curli secretion complex / curli assembly / protein secretion by the type VIII secretion system / protein transmembrane transport / single-species biofilm formation / cell outer membrane / outer membrane-bounded periplasmic space / identical protein binding / plasma membrane

Domain/homology:

ABC-type transport auxiliary lipoprotein component / Curli production assembly/transport component CsgG / Curli production assembly/transport component CsgG / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

Curli production assembly/transport component CsgG

• Biological species: ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
• Authors: Goyal, P. / Krasteva, P.V. / Gerven, N.V. / Gubellini, F. / Broeck, I.V.D. / Troupiotis-Tsailaki, A. / Jonckheere, W. / Pehau-Arnaudet, G. / Pinkner, J.S. / Chapman, M.R. / Hultgren, S.J. / Howorka, S. / Fronzes, R. / Remaut, H.
• Citation: Journal: Nature / Year: 2014; Title: Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG.; Authors: Parveen Goyal / Petya V Krasteva / Nani Van Gerven / Francesca Gubellini / Imke Van den Broeck / Anastassia Troupiotis-Tsaïlaki / Wim Jonckheere / Gérard Péhau-Arnaudet / Jerome S Pinkner / Matthew R Chapman / Scott J Hultgren / Stefan Howorka / Rémi Fronzes / Han Remaut / ; Abstract: Curli are functional amyloid fibres that constitute the major protein component of the extracellular matrix in pellicle biofilms formed by Bacteroidetes and Proteobacteria (predominantly of the α and γ classes). They provide a fitness advantage in pathogenic strains and induce a strong pro-inflammatory response during bacteraemia. Curli formation requires a dedicated protein secretion machinery comprising the outer membrane lipoprotein CsgG and two soluble accessory proteins, CsgE and CsgF. Here we report the X-ray structure of Escherichia coli CsgG in a non-lipidated, soluble form as well as in its native membrane-extracted conformation. CsgG forms an oligomeric transport complex composed of nine anticodon-binding-domain-like units that give rise to a 36-stranded β-barrel that traverses the bilayer and is connected to a cage-like vestibule in the periplasm. The transmembrane and periplasmic domains are separated by a 0.9-nm channel constriction composed of three stacked concentric phenylalanine, asparagine and tyrosine rings that may guide the extended polypeptide substrate through the secretion pore. The specificity factor CsgE forms a nonameric adaptor that binds and closes off the periplasmic face of the secretion channel, creating a 24,000 Å(3) pre-constriction chamber. Our structural, functional and electrophysiological analyses imply that CsgG is an ungated, non-selective protein secretion channel that is expected to employ a diffusion-based, entropy-driven transport mechanism.

History

Deposition	Aug 4, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2014	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

• Remark 700: SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

Assembly

Deposited unit

A: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

B: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

C: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

D: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

E: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

F: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

G: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

H: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

I: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

J: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

K: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

L: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

M: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

N: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

O: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

P: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

Q: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

R: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

Summary:

• 520 kDa, 18 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	520,378	18
Polymers	520,378	18
Non-polymers	0	0
Water	0

1

A: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

B: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

C: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

D: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

E: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

F: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

G: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

H: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

I: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

Summary:

• defined by author&software
• 260 kDa, 9 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	260,189	9
Polymers	260,189	9
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	56740 Å2
ΔGint	-256.4 kcal/mol
Surface area	87290 Å2
Method	PISA

2

J: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

K: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

L: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

M: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

N: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

O: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

P: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

Q: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

R: CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

Summary:

• defined by author&software
• 260 kDa, 9 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	260,189	9
Polymers	260,189	9
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	56870 Å2
ΔGint	-258.5 kcal/mol
Surface area	86830 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	161.934, 372.847, 161.972
Angle α, β, γ (deg.)	90.00, 92.90, 90.00
Int Tables number	5
Space group name H-M	C121

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: 0 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 2 - 257 / Label seq-ID: 2 - 257

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

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.762, 0.01, 0.648), (-0.012, 1, -0.002), (-0.648, -0.006, 0.762)	-17.50403, 0.41453, 34.08517
2	given	(0.168, 0.008, 0.986), (-0.016, 1, -0.006), (-0.986, -0.014, 0.168)	-9.2343, 0.7364, 71.23841
3	given	(-0.503, 0.864), (-0.022, 1, -0.013), (-0.864, -0.025, -0.503)	20.88865, 1.24095, 94.27494
4	given	(-0.94, -0.009, 0.342), (-0.017, 1, -0.02), (-0.342, -0.025, -0.939)	58.90655, 1.4501, 92.7235
5	given	(-0.938, -0.015, -0.345), (-0.007, 1, -0.025), (0.345, -0.021, -0.938)	87.07927, 1.34548, 66.84988
6	given	(-0.496, -0.025, -0.868), (1, -0.029), (0.868, -0.014, -0.496)	91.79681, 1.11549, 29.04159
7	given	(0.18, -0.024, -0.983), (0.001, 1, -0.024), (0.984, 0.004, 0.18)	71.20045, 0.79269, -2.83411
8	given	(0.769, -0.013, -0.639), (0.005, 1, -0.014), (0.639, 0.007, 0.769)	35.00981, 0.23753, -14.33744
9	given	(-0.974, -0.004, -0.227), (-0.002, -1, 0.023), (-0.227, 0.023, 0.974)	83.29317, -0.07177, 9.79241

Components

#1: Protein

A B C D E F G H I J K L M N O P Q R
CURLI PRODUCTION ASSEMBLY/TRANSPORT COMPONENT CSGG

Details:

Mass: 28909.893 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: LIPOPROTEIN
Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100 (bacteria)
Plasmid: PASK-IBA3PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEA2

• Sequence details: MATURE CSGG, MEMBRANE FORM

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 4.52 ų/Da / Density % sol: 73 %; Description: DATA WERE ANISOTROPICALLY SCALED TO 3.6, 3.7 AND 3.8 ANGSTROM ALONG RECIPROCAL DIRECTIONS A, B AND C.
• Crystal grow: pH: 8.5 ; Details: 100 MM TRIS-HCL PH 8.0, 8% PEG 4000, 100 MM NACL AND 500 MM MGCL2

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2011
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9763 Å / Relative weight: 1
• Reflection: Resolution: 3.6→30 Å / Num. obs: 102130 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / R_merge(I) obs: 0.16 / Net I/σ(I): 6.8
• Reflection shell: Resolution: 3.6→3.68 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.91 / Mean I/σ(I) obs: 1.89 / % possible all: 27.3

Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UV2

4uv2

Resolution: 3.59→30 Å / Cor.coef. F_o:F_c: 0.813 / Cor.coef. F_o:F_c free: 0.773 / SU B: 41.297 / SU ML: 0.619 / Cross valid method: THROUGHOUT / ESU R Free: 0.78 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.34903	5110	5 %	RANDOM
Rwork	0.29661	-	-	-
obs	0.29921	97020	91.5 %	-

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

Displacement parameters

B_iso mean: 115.072 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	2.18 Å2	0 Å2	-0.41 Å2
2-	-	-3.72 Å2	0 Å2
3-	-	-	1.56 Å2

Refinement step

Cycle: LAST / Resolution: 3.59→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34255	0	0	0	34255

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	34795
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	33905
X-RAY DIFFRACTION	r_angle_refined_deg	1.364	1.967	47212
X-RAY DIFFRACTION	r_angle_other_deg	1.3	3	77774
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.916	5	4397
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.665	24.832	1517
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.375	15	5991
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.873	15	221
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	5513
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	39624
X-RAY DIFFRACTION	r_gen_planes_other	0.013	0.02	7693
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	14054	0.07
1	2	B	14054	0.07
2	1	A	14007	0.07
2	2	C	14007	0.07
3	1	A	13844	0.08
3	2	D	13844	0.08
4	1	A	13795	0.08
4	2	E	13795	0.08
5	1	A	13886	0.07
5	2	F	13886	0.07
6	1	A	13831	0.08
6	2	G	13831	0.08
7	1	A	14063	0.07
7	2	H	14063	0.07
8	1	A	13947	0.07
8	2	I	13947	0.07
9	1	A	14013	0.08
9	2	J	14013	0.08
10	1	A	13954	0.07
10	2	K	13954	0.07
11	1	A	14151	0.06
11	2	L	14151	0.06
12	1	A	13857	0.08
12	2	M	13857	0.08
13	1	A	13997	0.08
13	2	N	13997	0.08
14	1	A	13817	0.08
14	2	O	13817	0.08
15	1	A	13844	0.08
15	2	P	13844	0.08
16	1	A	13849	0.08
16	2	Q	13849	0.08
17	1	A	13843	0.09
17	2	R	13843	0.09
18	1	B	14086	0.06
18	2	C	14086	0.06
19	1	B	14006	0.08
19	2	D	14006	0.08
20	1	B	13875	0.08
20	2	E	13875	0.08
21	1	B	13994	0.07
21	2	F	13994	0.07
22	1	B	13845	0.08
22	2	G	13845	0.08
23	1	B	14047	0.07
23	2	H	14047	0.07
24	1	B	14135	0.07
24	2	I	14135	0.07
25	1	B	14092	0.07
25	2	J	14092	0.07
26	1	B	14040	0.07
26	2	K	14040	0.07
27	1	B	14036	0.07
27	2	L	14036	0.07
28	1	B	13980	0.07
28	2	M	13980	0.07
29	1	B	14028	0.07
29	2	N	14028	0.07
30	1	B	13966	0.07
30	2	O	13966	0.07
31	1	B	13990	0.08
31	2	P	13990	0.08
32	1	B	13982	0.07
32	2	Q	13982	0.07
33	1	B	13879	0.09
33	2	R	13879	0.09
34	1	C	14026	0.07
34	2	D	14026	0.07
35	1	C	13979	0.08
35	2	E	13979	0.08
36	1	C	14085	0.06
36	2	F	14085	0.06
37	1	C	14041	0.07
37	2	G	14041	0.07
38	1	C	14152	0.06
38	2	H	14152	0.06
39	1	C	14157	0.07
39	2	I	14157	0.07
40	1	C	14138	0.06
40	2	J	14138	0.06
41	1	C	14157	0.06
41	2	K	14157	0.06
42	1	C	14096	0.07
42	2	L	14096	0.07
43	1	C	14070	0.07
43	2	M	14070	0.07
44	1	C	14224	0.06
44	2	N	14224	0.06
45	1	C	14031	0.07
45	2	O	14031	0.07
46	1	C	14082	0.07
46	2	P	14082	0.07
47	1	C	14127	0.06
47	2	Q	14127	0.06
48	1	C	13982	0.08
48	2	R	13982	0.08
49	1	D	13984	0.07
49	2	E	13984	0.07
50	1	D	14083	0.06
50	2	F	14083	0.06
51	1	D	14089	0.06
51	2	G	14089	0.06
52	1	D	14150	0.06
52	2	H	14150	0.06
53	1	D	14152	0.06
53	2	I	14152	0.06
54	1	D	14146	0.06
54	2	J	14146	0.06
55	1	D	14113	0.05
55	2	K	14113	0.05
56	1	D	13996	0.07
56	2	L	13996	0.07
57	1	D	14056	0.06
57	2	M	14056	0.06
58	1	D	14079	0.06
58	2	N	14079	0.06
59	1	D	14236	0.04
59	2	O	14236	0.04
60	1	D	14060	0.06
60	2	P	14060	0.06
61	1	D	14090	0.06
61	2	Q	14090	0.06
62	1	D	13893	0.08
62	2	R	13893	0.08
63	1	E	14015	0.07
63	2	F	14015	0.07
64	1	E	13918	0.08
64	2	G	13918	0.08
65	1	E	14029	0.07
65	2	H	14029	0.07
66	1	E	14091	0.07
66	2	I	14091	0.07
67	1	E	13966	0.08
67	2	J	13966	0.08
68	1	E	14010	0.07
68	2	K	14010	0.07
69	1	E	13962	0.08
69	2	L	13962	0.08
70	1	E	13976	0.08
70	2	M	13976	0.08
71	1	E	13974	0.08
71	2	N	13974	0.08
72	1	E	13991	0.07
72	2	O	13991	0.07
73	1	E	14014	0.08
73	2	P	14014	0.08
74	1	E	14012	0.08
74	2	Q	14012	0.08
75	1	E	13893	0.09
75	2	R	13893	0.09
76	1	F	14018	0.07
76	2	G	14018	0.07
77	1	F	14125	0.05
77	2	H	14125	0.05
78	1	F	14187	0.05
78	2	I	14187	0.05
79	1	F	14138	0.05
79	2	J	14138	0.05
80	1	F	14148	0.05
80	2	K	14148	0.05
81	1	F	14119	0.06
81	2	L	14119	0.06
82	1	F	14110	0.06
82	2	M	14110	0.06
83	1	F	14137	0.06
83	2	N	14137	0.06
84	1	F	14100	0.06
84	2	O	14100	0.06
85	1	F	14130	0.06
85	2	P	14130	0.06
86	1	F	14256	0.05
86	2	Q	14256	0.05
87	1	F	13980	0.07
87	2	R	13980	0.07
88	1	G	14123	0.06
88	2	H	14123	0.06
89	1	G	14097	0.06
89	2	I	14097	0.06
90	1	G	14111	0.06
90	2	J	14111	0.06
91	1	G	14134	0.06
91	2	K	14134	0.06
92	1	G	13951	0.07
92	2	L	13951	0.07
93	1	G	13960	0.07
93	2	M	13960	0.07
94	1	G	14068	0.07
94	2	N	14068	0.07
95	1	G	14070	0.07
95	2	O	14070	0.07
96	1	G	14026	0.07
96	2	P	14026	0.07
97	1	G	14026	0.07
97	2	Q	14026	0.07
98	1	G	14072	0.07
98	2	R	14072	0.07
99	1	H	14223	0.06
99	2	I	14223	0.06
100	1	H	14384	0.05
100	2	J	14384	0.05
101	1	H	14322	0.05
101	2	K	14322	0.05
102	1	H	14077	0.06
102	2	L	14077	0.06
103	1	H	14095	0.06
103	2	M	14095	0.06
104	1	H	14233	0.06
104	2	N	14233	0.06
105	1	H	14090	0.06
105	2	O	14090	0.06
106	1	H	14099	0.07
106	2	P	14099	0.07
107	1	H	14125	0.06
107	2	Q	14125	0.06
108	1	H	14070	0.07
108	2	R	14070	0.07
109	1	I	14261	0.05
109	2	J	14261	0.05
110	1	I	14313	0.05
110	2	K	14313	0.05
111	1	I	14106	0.07
111	2	L	14106	0.07
112	1	I	14145	0.06
112	2	M	14145	0.06
113	1	I	14170	0.06
113	2	N	14170	0.06
114	1	I	14123	0.06
114	2	O	14123	0.06
115	1	I	14171	0.06
115	2	P	14171	0.06
116	1	I	14206	0.06
116	2	Q	14206	0.06
117	1	I	14079	0.07
117	2	R	14079	0.07
118	1	J	14399	0.03
118	2	K	14399	0.03
119	1	J	14049	0.07
119	2	L	14049	0.07
120	1	J	14098	0.06
120	2	M	14098	0.06
121	1	J	14205	0.06
121	2	N	14205	0.06
122	1	J	14044	0.06
122	2	O	14044	0.06
123	1	J	14098	0.06
123	2	P	14098	0.06
124	1	J	14149	0.05
124	2	Q	14149	0.05
125	1	J	14109	0.07
125	2	R	14109	0.07
126	1	K	14082	0.06
126	2	L	14082	0.06
127	1	K	14100	0.06
127	2	M	14100	0.06
128	1	K	14240	0.06
128	2	N	14240	0.06
129	1	K	14079	0.06
129	2	O	14079	0.06
130	1	K	14100	0.06
130	2	P	14100	0.06
131	1	K	14154	0.06
131	2	Q	14154	0.06
132	1	K	14134	0.07
132	2	R	14134	0.07
133	1	L	14102	0.07
133	2	M	14102	0.07
134	1	L	14058	0.07
134	2	N	14058	0.07
135	1	L	14060	0.06
135	2	O	14060	0.06
136	1	L	14096	0.06
136	2	P	14096	0.06
137	1	L	14091	0.07
137	2	Q	14091	0.07
138	1	L	13900	0.08
138	2	R	13900	0.08
139	1	M	14102	0.06
139	2	N	14102	0.06
140	1	M	14197	0.05
140	2	O	14197	0.05
141	1	M	14217	0.06
141	2	P	14217	0.06
142	1	M	14295	0.05
142	2	Q	14295	0.05
143	1	M	14055	0.07
143	2	R	14055	0.07
144	1	N	14116	0.06
144	2	O	14116	0.06
145	1	N	14071	0.07
145	2	P	14071	0.07
146	1	N	14145	0.06
146	2	Q	14145	0.06
147	1	N	14069	0.08
147	2	R	14069	0.08
148	1	O	14245	0.05
148	2	P	14245	0.05
149	1	O	14253	0.05
149	2	Q	14253	0.05
150	1	O	14058	0.07
150	2	R	14058	0.07
151	1	P	14276	0.05
151	2	Q	14276	0.05
152	1	P	14050	0.08
152	2	R	14050	0.08
153	1	Q	14139	0.07
153	2	R	14139	0.07

LS refinement shell

Resolution: 3.587→3.68 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.403	75	-
Rwork	0.334	1429	-
obs	-	-	18.18 %