PDB-4qfe: Crystal Structure of an Enoyl-CoA hydratase from Mycobacterium sm...

Basic information

• Entry: Database: PDB / ID: 4qfe
• Title: Crystal Structure of an Enoyl-CoA hydratase from Mycobacterium smegmatis
• Components: Enoyl-CoA hydratase
• Keywords: LYASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / hydratase

Function / homology

Function:

enoyl-CoA hydratase activity

Domain/homology:

Helix Hairpins - #2460 / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta

Component:

ETHANOL / PHOSPHATE ION / Enoyl-CoA hydratase

• Biological species: Mycobacterium smegmatis (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
• Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Citation: Journal: TO BE PUBLISHED; Title: Crystal Structure of an Enoyl-CoA hydratase from Mycobacterium smegmatis; Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D.

History

Deposition	May 20, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 4, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

Assembly

Deposited unit

A: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

C: Enoyl-CoA hydratase

D: Enoyl-CoA hydratase

E: Enoyl-CoA hydratase

F: Enoyl-CoA hydratase

G: Enoyl-CoA hydratase

H: Enoyl-CoA hydratase

I: Enoyl-CoA hydratase

J: Enoyl-CoA hydratase

K: Enoyl-CoA hydratase

L: Enoyl-CoA hydratase

hetero molecules

Summary:

• 328 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	327,985	54
Polymers	325,435	12
Non-polymers	2,550	42
Water	26,572	1475

1

A: Enoyl-CoA hydratase

D: Enoyl-CoA hydratase

F: Enoyl-CoA hydratase

hetero molecules

Summary:

• defined by software
• 81.9 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	81,911	12
Polymers	81,359	3
Non-polymers	552	9
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	9960 Å2
ΔGint	-40 kcal/mol
Surface area	24300 Å2
Method	PISA

2

B: Enoyl-CoA hydratase

E: Enoyl-CoA hydratase

H: Enoyl-CoA hydratase

hetero molecules

Summary:

• defined by software
• 81.8 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	81,804	10
Polymers	81,359	3
Non-polymers	445	7
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	10500 Å2
ΔGint	-48 kcal/mol
Surface area	23820 Å2
Method	PISA

3

C: Enoyl-CoA hydratase

J: Enoyl-CoA hydratase

K: Enoyl-CoA hydratase

hetero molecules

Summary:

• defined by software
• 82.1 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	82,065	15
Polymers	81,359	3
Non-polymers	706	12
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	11220 Å2
ΔGint	-18 kcal/mol
Surface area	23760 Å2
Method	PISA

4

G: Enoyl-CoA hydratase

I: Enoyl-CoA hydratase

L: Enoyl-CoA hydratase

hetero molecules

Summary:

• defined by software
• 82.2 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	82,206	17
Polymers	81,359	3
Non-polymers	847	14
Water	54	3

Symmetry operations:

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

Calculated values:

Buried area	10950 Å2
ΔGint	-32 kcal/mol
Surface area	23640 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	78.290, 86.580, 106.160
Angle α, β, γ (deg.)	84.96, 73.62, 83.18
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	E
1	3	A
2	3	F
1	4	A
2	4	G
1	5	A
2	5	H
1	6	A
2	6	I
1	7	A
2	7	J
1	8	A
2	8	C
1	9	A
2	9	D
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	E
1	13	B
2	13	F
1	14	B
2	14	G
1	15	B
2	15	H
1	16	B
2	16	I
1	17	B
2	17	J
1	18	B
2	18	C
1	19	B
2	19	D
1	20	B
2	20	K
1	21	B
2	21	L
1	22	E
2	22	F
1	23	E
2	23	G
1	24	E
2	24	H
1	25	E
2	25	I
1	26	E
2	26	J
1	27	E
2	27	C
1	28	E
2	28	D
1	29	E
2	29	K
1	30	E
2	30	L
1	31	F
2	31	G
1	32	F
2	32	H
1	33	F
2	33	I
1	34	F
2	34	J
1	35	F
2	35	C
1	36	F
2	36	D
1	37	F
2	37	K
1	38	F
2	38	L
1	39	G
2	39	H
1	40	G
2	40	I
1	41	G
2	41	J
1	42	G
2	42	C
1	43	G
2	43	D
1	44	G
2	44	K
1	45	G
2	45	L
1	46	H
2	46	I
1	47	H
2	47	J
1	48	H
2	48	C
1	49	H
2	49	D
1	50	H
2	50	K
1	51	H
2	51	L
1	52	I
2	52	J
1	53	I
2	53	C
1	54	I
2	54	D
1	55	I
2	55	K
1	56	I
2	56	L
1	57	J
2	57	C
1	58	J
2	58	D
1	59	J
2	59	K
1	60	J
2	60	L
1	61	C
2	61	D
1	62	C
2	62	K
1	63	C
2	63	L
1	64	D
2	64	K
1	65	D
2	65	L
1	66	K
2	66	L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	ILE	ILE	A	A	2 - 229	7 - 234
2	1	SER	SER	ILE	ILE	B	B	2 - 229	7 - 234
1	2	VAL	VAL	ILE	ILE	A	A	1 - 229	6 - 234
2	2	VAL	VAL	ILE	ILE	E	E	1 - 229	6 - 234
1	3	PRO	PRO	ILE	ILE	A	A	4 - 229	9 - 234
2	3	PRO	PRO	ILE	ILE	F	F	4 - 229	9 - 234
1	4	GLU	GLU	ILE	ILE	A	A	3 - 229	8 - 234
2	4	GLU	GLU	ILE	ILE	G	G	3 - 229	8 - 234
1	5	GLU	GLU	ILE	ILE	A	A	3 - 229	8 - 234
2	5	GLU	GLU	ILE	ILE	H	H	3 - 229	8 - 234
1	6	SER	SER	ILE	ILE	A	A	2 - 229	7 - 234
2	6	SER	SER	ILE	ILE	I	I	2 - 229	7 - 234
1	7	GLU	GLU	ILE	ILE	A	A	3 - 229	8 - 234
2	7	GLU	GLU	ILE	ILE	J	J	3 - 229	8 - 234
1	8	SER	SER	ILE	ILE	A	A	2 - 229	7 - 234
2	8	SER	SER	ILE	ILE	C	C	2 - 229	7 - 234
1	9	SER	SER	ILE	ILE	A	A	2 - 229	7 - 234
2	9	SER	SER	ILE	ILE	D	D	2 - 229	7 - 234
1	10	PRO	PRO	SER	SER	A	A	4 - 228	9 - 233
2	10	PRO	PRO	SER	SER	K	K	4 - 228	9 - 233
1	11	GLU	GLU	ILE	ILE	A	A	3 - 229	8 - 234
2	11	GLU	GLU	ILE	ILE	L	L	3 - 229	8 - 234
1	12	SER	SER	ILE	ILE	B	B	2 - 229	7 - 234
2	12	SER	SER	ILE	ILE	E	E	2 - 229	7 - 234
1	13	PRO	PRO	SER	SER	B	B	4 - 228	9 - 233
2	13	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
1	14	GLU	GLU	SER	SER	B	B	3 - 228	8 - 233
2	14	GLU	GLU	SER	SER	G	G	3 - 228	8 - 233
1	15	GLU	GLU	SER	SER	B	B	3 - 228	8 - 233
2	15	GLU	GLU	SER	SER	H	H	3 - 228	8 - 233
1	16	SER	SER	ILE	ILE	B	B	2 - 229	7 - 234
2	16	SER	SER	ILE	ILE	I	I	2 - 229	7 - 234
1	17	GLU	GLU	SER	SER	B	B	3 - 228	8 - 233
2	17	GLU	GLU	SER	SER	J	J	3 - 228	8 - 233
1	18	SER	SER	SER	SER	B	B	2 - 228	7 - 233
2	18	SER	SER	SER	SER	C	C	2 - 228	7 - 233
1	19	SER	SER	SER	SER	B	B	2 - 228	7 - 233
2	19	SER	SER	SER	SER	D	D	2 - 228	7 - 233
1	20	PRO	PRO	SER	SER	B	B	4 - 228	9 - 233
2	20	PRO	PRO	SER	SER	K	K	4 - 228	9 - 233
1	21	GLU	GLU	SER	SER	B	B	3 - 228	8 - 233
2	21	GLU	GLU	SER	SER	L	L	3 - 228	8 - 233
1	22	PRO	PRO	ILE	ILE	E	E	4 - 229	9 - 234
2	22	PRO	PRO	ILE	ILE	F	F	4 - 229	9 - 234
1	23	GLU	GLU	ILE	ILE	E	E	3 - 229	8 - 234
2	23	GLU	GLU	ILE	ILE	G	G	3 - 229	8 - 234
1	24	GLU	GLU	ILE	ILE	E	E	3 - 229	8 - 234
2	24	GLU	GLU	ILE	ILE	H	H	3 - 229	8 - 234
1	25	SER	SER	ILE	ILE	E	E	2 - 229	7 - 234
2	25	SER	SER	ILE	ILE	I	I	2 - 229	7 - 234
1	26	GLU	GLU	ILE	ILE	E	E	3 - 229	8 - 234
2	26	GLU	GLU	ILE	ILE	J	J	3 - 229	8 - 234
1	27	SER	SER	ILE	ILE	E	E	2 - 229	7 - 234
2	27	SER	SER	ILE	ILE	C	C	2 - 229	7 - 234
1	28	SER	SER	ILE	ILE	E	E	2 - 229	7 - 234
2	28	SER	SER	ILE	ILE	D	D	2 - 229	7 - 234
1	29	PRO	PRO	SER	SER	E	E	4 - 228	9 - 233
2	29	PRO	PRO	SER	SER	K	K	4 - 228	9 - 233
1	30	GLU	GLU	ILE	ILE	E	E	3 - 229	8 - 234
2	30	GLU	GLU	ILE	ILE	L	L	3 - 229	8 - 234
1	31	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	31	PRO	PRO	SER	SER	G	G	4 - 228	9 - 233
1	32	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	32	PRO	PRO	SER	SER	H	H	4 - 228	9 - 233
1	33	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	33	PRO	PRO	SER	SER	I	I	4 - 228	9 - 233
1	34	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	34	PRO	PRO	SER	SER	J	J	4 - 228	9 - 233
1	35	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	35	PRO	PRO	SER	SER	C	C	4 - 228	9 - 233
1	36	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	36	PRO	PRO	SER	SER	D	D	4 - 228	9 - 233
1	37	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	37	PRO	PRO	SER	SER	K	K	4 - 228	9 - 233
1	38	PRO	PRO	SER	SER	F	F	4 - 228	9 - 233
2	38	PRO	PRO	SER	SER	L	L	4 - 228	9 - 233
1	39	GLU	GLU	ILE	ILE	G	G	3 - 229	8 - 234
2	39	GLU	GLU	ILE	ILE	H	H	3 - 229	8 - 234
1	40	GLU	GLU	SER	SER	G	G	3 - 228	8 - 233
2	40	GLU	GLU	SER	SER	I	I	3 - 228	8 - 233
1	41	GLU	GLU	SER	SER	G	G	3 - 228	8 - 233
2	41	GLU	GLU	SER	SER	J	J	3 - 228	8 - 233
1	42	GLU	GLU	SER	SER	G	G	3 - 228	8 - 233
2	42	GLU	GLU	SER	SER	C	C	3 - 228	8 - 233
1	43	GLU	GLU	SER	SER	G	G	3 - 228	8 - 233
2	43	GLU	GLU	SER	SER	D	D	3 - 228	8 - 233
1	44	PRO	PRO	SER	SER	G	G	4 - 228	9 - 233
2	44	PRO	PRO	SER	SER	K	K	4 - 228	9 - 233
1	45	GLU	GLU	SER	SER	G	G	3 - 228	8 - 233
2	45	GLU	GLU	SER	SER	L	L	3 - 228	8 - 233
1	46	GLU	GLU	SER	SER	H	H	3 - 228	8 - 233
2	46	GLU	GLU	SER	SER	I	I	3 - 228	8 - 233
1	47	GLU	GLU	SER	SER	H	H	3 - 228	8 - 233
2	47	GLU	GLU	SER	SER	J	J	3 - 228	8 - 233
1	48	GLU	GLU	SER	SER	H	H	3 - 228	8 - 233
2	48	GLU	GLU	SER	SER	C	C	3 - 228	8 - 233
1	49	GLU	GLU	SER	SER	H	H	3 - 228	8 - 233
2	49	GLU	GLU	SER	SER	D	D	3 - 228	8 - 233
1	50	PRO	PRO	SER	SER	H	H	4 - 228	9 - 233
2	50	PRO	PRO	SER	SER	K	K	4 - 228	9 - 233
1	51	GLU	GLU	SER	SER	H	H	3 - 228	8 - 233
2	51	GLU	GLU	SER	SER	L	L	3 - 228	8 - 233
1	52	GLU	GLU	SER	SER	I	I	3 - 228	8 - 233
2	52	GLU	GLU	SER	SER	J	J	3 - 228	8 - 233
1	53	SER	SER	SER	SER	I	I	2 - 228	7 - 233
2	53	SER	SER	SER	SER	C	C	2 - 228	7 - 233
1	54	SER	SER	SER	SER	I	I	2 - 228	7 - 233
2	54	SER	SER	SER	SER	D	D	2 - 228	7 - 233
1	55	PRO	PRO	SER	SER	I	I	4 - 228	9 - 233
2	55	PRO	PRO	SER	SER	K	K	4 - 228	9 - 233
1	56	GLU	GLU	SER	SER	I	I	3 - 228	8 - 233
2	56	GLU	GLU	SER	SER	L	L	3 - 228	8 - 233
1	57	GLU	GLU	ILE	ILE	J	J	3 - 229	8 - 234
2	57	GLU	GLU	ILE	ILE	C	C	3 - 229	8 - 234
1	58	GLU	GLU	ILE	ILE	J	J	3 - 229	8 - 234
2	58	GLU	GLU	ILE	ILE	D	D	3 - 229	8 - 234
1	59	PRO	PRO	ILE	ILE	J	J	4 - 229	9 - 234
2	59	PRO	PRO	ILE	ILE	K	K	4 - 229	9 - 234
1	60	GLU	GLU	ILE	ILE	J	J	3 - 229	8 - 234
2	60	GLU	GLU	ILE	ILE	L	L	3 - 229	8 - 234
1	61	SER	SER	ILE	ILE	C	C	2 - 229	7 - 234
2	61	SER	SER	ILE	ILE	D	D	2 - 229	7 - 234
1	62	PRO	PRO	ILE	ILE	C	C	4 - 229	9 - 234
2	62	PRO	PRO	ILE	ILE	K	K	4 - 229	9 - 234
1	63	GLU	GLU	ILE	ILE	C	C	3 - 229	8 - 234
2	63	GLU	GLU	ILE	ILE	L	L	3 - 229	8 - 234
1	64	PRO	PRO	SER	SER	D	D	4 - 230	9 - 235
2	64	PRO	PRO	SER	SER	K	K	4 - 230	9 - 235
1	65	GLU	GLU	SER	SER	D	D	3 - 230	8 - 235
2	65	GLU	GLU	SER	SER	L	L	3 - 230	8 - 235
1	66	PRO	PRO	SER	SER	K	K	4 - 230	9 - 235
2	66	PRO	PRO	SER	SER	L	L	4 - 230	9 - 235

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

Components

Protein , 1 types, 12 molecules A B C D E F G H I J K L

#1: Protein

A B C D E F G H I J K L
Enoyl-CoA hydratase / Enoyl-CoA hydratase/isomerase

Details:

Mass: 27119.592 Da / Num. of mol.: 12 / Fragment: MysmA.00386.a.A1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: echA5, MSMEG_1390, MSMEI_1352 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QS88, enoyl-CoA hydratase

Non-polymers , 5 types, 1517 molecules

#2: Chemical

A-301 A-302 A-303 A-304 B-302 B-303 C-301 C-302 D-302 E-301 F-301 F-302 G-301 G-302 G-303 I-302 I-303 I-304 I-305 I-306 ...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C₂H₆O₂

#3: Chemical

A-305 B-305 G-304 J-307
ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na

#4: Chemical

B-301 I-301 ChemComp-EOH / ETHANOL

Details:

Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O

#5: Chemical

B-304 D-301 G-305 H-301
ChemComp-PO4 / PHOSPHATE ION

Details:

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 1475 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.1 ų/Da / Density % sol: 41.51 %
• Crystal grow: Method: vapor diffusion, sitting drop / pH: 4.2 ; Details: 40% reagent alcohol, 0.1M sodium phosphate dibasic/ citric acid, pH=4.2, 5% PEG-1000, VAPOR DIFFUSION, SITTING DROP

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
• Detector: Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2010
• Radiation: Monochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9795 Å / Relative weight: 1
• Reflection: Resolution: 1.95→50 Å / Num. all: 193399 / Num. obs: 186042 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / R_merge(I) obs: 0.064 / Net I/σ(I): 10.42

Reflection shell

Resolution (Å)	Highest resolution (Å)	Rmerge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.95-2		0.394	2.48	1	95.9
2-2.06		0.319	3.1	1	96.1
2.06-2.12		0.258	3.77	1	96.1
2.12-2.18		0.2	4.81	1	95.9
2.18-2.25		0.184	5.24	1	96
2.25-2.33		0.148	6.33	1	96.1
2.33-2.42		0.123	7.45	1	96.1
2.42-2.52		0.115	8	1	96
2.52-2.63		0.094	9.26	1	96.7
2.63-2.76		0.083	10.36	1	96.6
2.76-2.91		0.068	12.31	1	96.3
2.91-3.08		0.055	14.51	1	96.7
3.08-3.3		0.047	16.96	1	96.4
3.3-3.56		0.041	19.14	1	95.6
3.56-3.9		0.036	21.28	1	96
3.9-4.36		0.034	22.13	1	95.3
4.36-5.03		0.031	22.64	1	96.5
5.03-6.17		0.033	22.16	1	96.9
6.17-8.72		0.031	23.61	1	97.5
	8.72	0.029	26.19	1	97.3

Phasing

• Phasing: Method: molecular replacement

Processing

Software

Name	Version	Classification	NB
XSCALE		data scaling
REFMAC	5.8.0069	refinement
PDB_EXTRACT	3.14	data extraction
ALS	collection software	data collection
BALBES		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.316 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.922 / SU B: 8.629 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.22343	9247	5 %	RANDOM
Rwork	0.19733	-	-	-
obs	0.19864	176795	96.25 %	-
all	-	195289	-	-

• 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: 23.934 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.43 Å2	-0.07 Å2	0.1 Å2
2-	-	0.03 Å2	-0.06 Å2
3-	-	-	-0.36 Å2

Refinement step

Cycle: LAST / Resolution: 1.95→46.316 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19774	0	158	1475	21407

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	20364
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	19258
X-RAY DIFFRACTION	r_angle_refined_deg	1.443	1.962	27698
X-RAY DIFFRACTION	r_angle_other_deg	1.522	3	43975
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.52	5	2751
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.245	23.294	856
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.943	15	2909
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.915	15	198
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	3169
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	23839
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	4537
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	0.964	1.418	10947
X-RAY DIFFRACTION	r_mcbond_other	0.964	1.417	10946
X-RAY DIFFRACTION	r_mcangle_it	1.533	2.118	13669
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.479	1.594	9417
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	12148	0.07
1	2	B	12148	0.07
2	1	A	12253	0.06
2	2	E	12253	0.06
3	1	A	12039	0.08
3	2	F	12039	0.08
4	1	A	12109	0.07
4	2	G	12109	0.07
5	1	A	11883	0.07
5	2	H	11883	0.07
6	1	A	12070	0.08
6	2	I	12070	0.08
7	1	A	12127	0.08
7	2	J	12127	0.08
8	1	A	12060	0.08
8	2	C	12060	0.08
9	1	A	12018	0.08
9	2	D	12018	0.08
10	1	A	11996	0.07
10	2	K	11996	0.07
11	1	A	11867	0.07
11	2	L	11867	0.07
12	1	B	12107	0.08
12	2	E	12107	0.08
13	1	B	12662	0.07
13	2	F	12662	0.07
14	1	B	12782	0.06
14	2	G	12782	0.06
15	1	B	12416	0.07
15	2	H	12416	0.07
16	1	B	12637	0.08
16	2	I	12637	0.08
17	1	B	12763	0.07
17	2	J	12763	0.07
18	1	B	12656	0.07
18	2	C	12656	0.07
19	1	B	12815	0.06
19	2	D	12815	0.06
20	1	B	12473	0.07
20	2	K	12473	0.07
21	1	B	12364	0.06
21	2	L	12364	0.06
22	1	E	11933	0.08
22	2	F	11933	0.08
23	1	E	11946	0.09
23	2	G	11946	0.09
24	1	E	11884	0.08
24	2	H	11884	0.08
25	1	E	12057	0.08
25	2	I	12057	0.08
26	1	E	12047	0.08
26	2	J	12047	0.08
27	1	E	12018	0.08
27	2	C	12018	0.08
28	1	E	12039	0.08
28	2	D	12039	0.08
29	1	E	12044	0.07
29	2	K	12044	0.07
30	1	E	11869	0.07
30	2	L	11869	0.07
31	1	F	12499	0.07
31	2	G	12499	0.07
32	1	F	12558	0.05
32	2	H	12558	0.05
33	1	F	12436	0.08
33	2	I	12436	0.08
34	1	F	12625	0.07
34	2	J	12625	0.07
35	1	F	12460	0.07
35	2	C	12460	0.07
36	1	F	12435	0.08
36	2	D	12435	0.08
37	1	F	12447	0.07
37	2	K	12447	0.07
38	1	F	12108	0.07
38	2	L	12108	0.07
39	1	G	12446	0.06
39	2	H	12446	0.06
40	1	G	12603	0.07
40	2	I	12603	0.07
41	1	G	12884	0.05
41	2	J	12884	0.05
42	1	G	12563	0.07
42	2	C	12563	0.07
43	1	G	12497	0.07
43	2	D	12497	0.07
44	1	G	12412	0.07
44	2	K	12412	0.07
45	1	G	12268	0.07
45	2	L	12268	0.07
46	1	H	12208	0.07
46	2	I	12208	0.07
47	1	H	12391	0.07
47	2	J	12391	0.07
48	1	H	12225	0.08
48	2	C	12225	0.08
49	1	H	12254	0.07
49	2	D	12254	0.07
50	1	H	12247	0.06
50	2	K	12247	0.06
51	1	H	12158	0.06
51	2	L	12158	0.06
52	1	I	12718	0.07
52	2	J	12718	0.07
53	1	I	12626	0.06
53	2	C	12626	0.06
54	1	I	12576	0.07
54	2	D	12576	0.07
55	1	I	12512	0.06
55	2	K	12512	0.06
56	1	I	12273	0.06
56	2	L	12273	0.06
57	1	J	12810	0.07
57	2	C	12810	0.07
58	1	J	12873	0.07
58	2	D	12873	0.07
59	1	J	12799	0.06
59	2	K	12799	0.06
60	1	J	12574	0.07
60	2	L	12574	0.07
61	1	C	12515	0.07
61	2	D	12515	0.07
62	1	C	12460	0.06
62	2	K	12460	0.06
63	1	C	12251	0.06
63	2	L	12251	0.06
64	1	D	12519	0.06
64	2	K	12519	0.06
65	1	D	12298	0.06
65	2	L	12298	0.06
66	1	K	12424	0.06
66	2	L	12424	0.06

LS refinement shell

Resolution: 1.95→2.001 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.299	711	-
Rwork	0.27	13010	-
obs	-	-	95.9 %

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	0.8583	-0.1317	-0.2239	1.0219	0.4925	0.9051	0.0287	-0.0189	0.127	-0.0992	0.0245	-0.0541	-0.1415	0.0351	-0.0532	0.0633	0.0085	0.0182	0.0404	0.0426	0.1263	54.1788	37.1351	78.4666
2	0.1053	0.1232	-0.0885	0.6212	-0.0533	0.1934	0.0468	0.0541	0.0464	0.0581	-0.0279	0.0291	-0.0559	-0.0361	-0.0189	0.0301	0.0147	0.0017	0.0691	0.0213	0.1221	48.7979	24.2639	82.615
3	2.4345	1.1884	-1.5649	3.9016	3.3551	7.8548	-0.0162	0.3013	0.02	-0.1215	0.0671	0.1113	0.0408	-0.1899	-0.0509	0.0325	0.0204	-0.0434	0.122	0.0216	0.1039	36.2614	9.7962	67.7898
4	0.4227	-0.0028	-0.7875	0.4225	0.1897	1.9746	-0.1016	-0.1269	-0.1673	0.2594	-0.0198	-0.0679	0.2967	-0.0024	0.1214	0.1825	0.0203	-0.0009	0.1632	0.1393	0.1369	60.9397	26.2016	119.4747
5	0.0047	-0.0321	-0.0472	1.549	0.2921	1.5118	0.0236	-0.0141	-0.0031	0.1488	0.0651	-0.1063	-0.0343	-0.0397	-0.0887	0.128	-0.0278	-0.0151	0.1366	0.0822	0.0698	58.4627	31.8723	119.3228
6	0.3952	-0.0548	-0.2305	0.4232	0.1889	0.2552	0.0068	-0.077	-0.0647	0.0886	-0.017	-0.0845	0.0262	0.0227	0.0102	0.0535	0.0083	-0.026	0.0769	0.0372	0.101	65.3655	38.7805	109.6662
7	0.7517	1.0816	-0.4642	2.0759	-0.1013	1.0677	-0.1072	0.0998	-0.1725	-0.0339	0.0843	-0.2295	0.2707	-0.0069	0.023	0.121	0.0562	-0.0108	0.1155	-0.0888	0.105	87.1002	-31.2648	38.8675
8	0.1394	0.1114	0.044	0.3584	0.391	0.6715	-0.0046	0.0322	0.0171	0.0277	-0.0197	0.0526	0.1259	0.0483	0.0243	0.0795	0.0247	0.0018	0.0716	-0.0184	0.0827	82.1257	-20.1868	47.3784
9	0.8793	0.7331	0.6963	1.6567	0.5665	0.7008	-0.0292	0.0852	0.0352	-0.1425	-0.023	-0.1365	0.0855	0.1793	0.0522	0.0947	0.0648	0.0428	0.179	0.0058	0.0429	98.5365	-12.2427	40.3886
10	0.3488	0.334	-0.5082	0.8157	0.1286	1.6389	-0.0508	0.0654	-0.0699	-0.1048	0.0396	-0.0282	0.0256	-0.0229	0.0111	0.0219	-0.0001	-0.0239	0.1191	-0.103	0.1628	44.9587	-13.254	66.2421
11	0.5086	0.0748	-0.1825	0.3966	-0.0226	0.0985	0.0049	0.0965	-0.0032	0.0075	-0.0016	0.0503	0.0166	-0.0219	-0.0034	0.0264	0.0021	-0.0134	0.0989	-0.0181	0.0997	47.3475	-0.4265	74.5284
12	1.6619	-0.8602	-0.3489	1.1264	-0.0288	0.2728	-0.0155	0.0292	-0.0555	-0.129	0.0755	0.0975	0.0658	-0.0989	-0.06	0.0325	-0.0208	-0.0338	0.0885	-0.0058	0.1438	29.8548	-5.4411	83.0449
13	0.8706	0.4046	-0.7727	1.5538	-0.4323	1.7167	0.0727	0.0105	0.141	0.1703	-0.0339	0.0046	-0.1959	-0.0101	-0.0388	0.0637	-0.0138	-0.0158	0.0432	-0.0417	0.1013	63.7338	78.2927	108.5272
14	0.4642	0.1031	0.2095	0.5571	0.1324	0.5259	0.0026	0.0166	0.049	-0.0227	0.017	-0.0648	0.0323	0.085	-0.0196	0.0371	-0.0132	-0.0205	0.0703	-0.0154	0.1162	67.4086	70.9861	103.3395
15	0.094	0.1672	-0.1288	0.988	-0.0855	0.2318	0.0161	-0.0442	0.0045	0.0219	-0.0189	-0.1018	-0.0426	0.0483	0.0028	0.0275	0.0008	-0.0252	0.0889	-0.0078	0.0927	65.5316	57.7244	106.5347
16	1.6557	0.6576	0.1099	2.162	0.152	0.9296	0.1656	-0.199	0.0699	0.4019	0.0339	0.2753	-0.0901	-0.2848	-0.1996	0.0952	0.0265	0.0922	0.1449	0.0347	0.1352	20.9269	8.6909	107.8678
17	0.3245	0.0733	-0.1647	0.3335	-0.1566	0.3942	0.0873	0.0236	-0.0196	0.0802	-0.0001	0.0585	-0.0089	-0.0461	-0.0871	0.0547	-0.0041	0.0175	0.0661	0.0025	0.134	30.0486	2.2242	98.1318
18	0.9621	0.5534	-0.3524	1.0804	-1.7436	3.4466	0.1711	0.1169	0.2913	0.206	0.0677	0.3006	-0.1936	-0.0707	-0.2388	0.0992	0.0236	0.11	0.0286	0.0024	0.2268	32.0475	21.88	93.9807
19	1.5036	0.5149	-0.8978	0.9482	-0.7358	0.7825	-0.2584	0.0904	0.0024	-0.183	0.1004	-0.2571	0.1821	-0.0853	0.158	0.1858	-0.0189	0.0124	0.0192	-0.0107	0.1037	36.8507	49.7304	110.395
20	0.493	0.0547	-0.33	0.5504	-0.0875	0.496	-0.0612	-0.0394	0.0145	-0.1039	0.0447	-0.0045	-0.0804	-0.06	0.0165	0.1179	0.0184	-0.0173	0.0471	-0.0061	0.0598	29.5128	54.7503	121.8408
21	1.2563	0.626	-0.5049	0.6556	-0.7921	1.2032	-0.2211	-0.0301	-0.138	-0.2847	0.0958	-0.1158	0.2309	-0.1898	0.1254	0.2425	-0.0217	0.0504	0.0448	-0.0224	0.0653	25.7419	35.0261	122.6498
22	1.5315	-0.7271	1.3223	3.2938	0.1724	1.4335	0.0895	0.217	-0.0748	-0.6182	0.0708	-0.4454	-0.0617	0.3418	-0.1603	0.1519	-0.0134	0.161	0.2033	-0.0223	0.2314	89.0546	43.9664	78.6046
23	0.0695	0.0163	0.0486	0.8381	0.1214	0.4886	-0.0146	-0.0422	-0.0655	-0.1589	0.0912	-0.2259	-0.0032	0.0402	-0.0766	0.0386	-0.0119	0.071	0.0518	-0.0075	0.1825	78.6527	43.6522	88.3531
24	3.3348	1.36	-0.3421	8.3694	-3.4243	7.2645	0.0599	-0.0677	0.1631	0.3121	-0.153	-0.3835	-0.1632	0.2921	0.093	0.0183	-0.0117	-0.0403	0.1217	-0.0266	0.1703	83.262	63.6922	105.3841
25	1.2595	-1.1865	-1.0034	2.4535	0.6846	0.8554	-0.1978	-0.003	-0.1505	0.0679	0.079	0.1728	0.1894	-0.033	0.1188	0.052	-0.0394	0.0176	0.134	0.0401	0.0756	14.3455	20.9708	147.2123
26	0.3407	0.2384	0.0481	1.1919	-0.4705	0.2794	-0.0484	-0.0199	-0.0041	-0.1226	0.0535	-0.064	0.0637	-0.0657	-0.0051	0.0601	-0.0221	-0.0111	0.1073	0.0229	0.0722	18.7675	26.3924	140.7161
27	0.2418	-0.0137	-0.1947	0.8777	-0.3618	0.4956	-0.0443	-0.0088	-0.0163	-0.0313	0.0229	-0.0341	-0.0024	-0.1254	0.0214	0.0394	0.0195	-0.0172	0.1113	0.0112	0.0575	17.9721	38.8175	140.2199
28	0.5476	-0.0579	-0.1404	0.5072	0.1804	0.5604	-0.0649	0.0039	0.0465	0.0645	-0.0477	0.0228	0.0194	-0.0005	0.1126	0.0328	0.0037	-0.0051	0.0645	0.0026	0.1129	75.8653	2.5135	73.3132
29	0.3098	-0.1418	-0.2543	0.3784	0.2342	0.4082	-0.0275	0.0892	0.0251	0.0492	-0.0092	0.028	0.0232	0.0251	0.0368	0.0311	-0.0104	-0.0078	0.0817	0.0153	0.0997	79.2802	-0.2215	60.4952
30	5.8578	4.6529	-2.1687	13.4991	1.1321	1.7492	-0.1433	-0.1819	-0.1604	0.4423	0.0058	0.0054	0.3863	0.1778	0.1376	0.2927	0.0951	0.035	0.0951	0.019	0.1481	91.085	-22.1566	61.1496
31	3.3157	-1.2447	-1.5706	0.5365	1.1457	5.2608	0.1497	0.1479	0.5121	-0.0854	0.0133	-0.1888	-0.2924	0.4857	-0.1631	0.0864	-0.1099	0.0178	0.2142	0.0719	0.1408	107.6474	17.2646	43.1756
32	0.3509	-0.1963	-0.1177	0.4559	0.2379	0.8101	0.0064	0.1038	0.0411	-0.0791	0.0128	-0.0356	-0.0813	0.1966	-0.0192	0.0268	-0.0417	-0.0044	0.142	0.046	0.0737	98.1493	6.9597	44.2279
33	1.1667	-1.5464	-1.3302	9.2338	0.9146	4.7298	-0.0672	-0.2449	0.089	0.409	0.1104	-0.1341	-0.0516	0.3495	-0.0433	0.0506	0.0042	-0.0461	0.1561	0.0188	0.0721	95.6288	3.0604	70.4043
34	4.4673	0.5158	-0.6896	0.8721	-1.2498	2.722	-0.1151	-0.4044	0.7278	0.2013	0.2431	0.3947	-0.8729	-0.6524	-0.1281	0.4244	0.2817	-0.2007	0.2379	-0.1013	0.4271	6.0438	72.9446	142.8109
35	0.3956	0.1946	-0.1635	0.7268	-0.3652	0.8313	0.0104	-0.0763	0.019	0.1111	0.0843	0.096	-0.2309	-0.2047	-0.0947	0.1008	0.1017	-0.0046	0.1227	-0.0096	0.0659	12.9835	60.4243	141.3504
36	2.0343	2.5629	-1.574	9.6694	1.8422	6.4325	-0.0528	0.2375	-0.078	-0.527	0.0425	0.1307	-0.4273	-0.3575	0.0103	0.1325	0.0434	-0.0512	0.1608	0.005	0.0643	14.2872	57.2155	115.2018

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 41
2	X-RAY DIFFRACTION	2	A	42 - 211
3	X-RAY DIFFRACTION	3	A	212 - 229
4	X-RAY DIFFRACTION	4	B	2 - 45
5	X-RAY DIFFRACTION	5	B	46 - 72
6	X-RAY DIFFRACTION	6	B	73 - 229
7	X-RAY DIFFRACTION	7	C	2 - 46
8	X-RAY DIFFRACTION	8	C	47 - 181
9	X-RAY DIFFRACTION	9	C	182 - 230
10	X-RAY DIFFRACTION	10	D	2 - 75
11	X-RAY DIFFRACTION	11	D	76 - 184
12	X-RAY DIFFRACTION	12	D	185 - 231
13	X-RAY DIFFRACTION	13	E	1 - 43
14	X-RAY DIFFRACTION	14	E	44 - 136
15	X-RAY DIFFRACTION	15	E	137 - 229
16	X-RAY DIFFRACTION	16	F	4 - 46
17	X-RAY DIFFRACTION	17	F	47 - 183
18	X-RAY DIFFRACTION	18	F	184 - 229
19	X-RAY DIFFRACTION	19	G	3 - 68
20	X-RAY DIFFRACTION	20	G	69 - 184
21	X-RAY DIFFRACTION	21	G	185 - 229
22	X-RAY DIFFRACTION	22	H	3 - 46
23	X-RAY DIFFRACTION	23	H	47 - 216
24	X-RAY DIFFRACTION	24	H	217 - 229
25	X-RAY DIFFRACTION	25	I	2 - 46
26	X-RAY DIFFRACTION	26	I	47 - 125
27	X-RAY DIFFRACTION	27	I	126 - 229
28	X-RAY DIFFRACTION	28	J	3 - 122
29	X-RAY DIFFRACTION	29	J	123 - 216
30	X-RAY DIFFRACTION	30	J	217 - 230
31	X-RAY DIFFRACTION	31	K	4 - 46
32	X-RAY DIFFRACTION	32	K	47 - 216
33	X-RAY DIFFRACTION	33	K	217 - 232
34	X-RAY DIFFRACTION	34	L	3 - 46
35	X-RAY DIFFRACTION	35	L	47 - 218
36	X-RAY DIFFRACTION	36	L	219 - 231