PDB-6ap4: Crystal structure of the DNA polymerase III subunit beta from Aci...

Basic information

• Entry: Database: PDB / ID: 6ap4
• Title: Crystal structure of the DNA polymerase III subunit beta from Acinetobacter baumannii
• Components: DNA polymerase III subunit beta
• Keywords: TRANSFERASE / DNA Binding / DNA Directed DNA Polymerase Activity

Function / homology

Function:

DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm

Domain/homology:

DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / Roll / Alpha Beta

Component:

Beta sliding clamp

• Biological species: Acinetobacter baumannii (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
• Authors: McGrath, A.E. / Oakley, A.J.
• Citation: Journal: J. Struct. Biol. / Year: 2018; Title: Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens.; Authors: McGrath, A.E. / Martyn, A.P. / Whittell, L.R. / Dawes, F.E. / Beck, J.L. / Dixon, N.E. / Kelso, M.J. / Oakley, A.J.

History

Deposition	Aug 16, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 7, 2018	Group: Data collection / Database references / Source and taxonomy Category: citation / entity_src_gen Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2	Dec 26, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: DNA polymerase III subunit beta

B: DNA polymerase III subunit beta

C: DNA polymerase III subunit beta

D: DNA polymerase III subunit beta

E: DNA polymerase III subunit beta

F: DNA polymerase III subunit beta

G: DNA polymerase III subunit beta

H: DNA polymerase III subunit beta

I: DNA polymerase III subunit beta

J: DNA polymerase III subunit beta

K: DNA polymerase III subunit beta

L: DNA polymerase III subunit beta

M: DNA polymerase III subunit beta

N: DNA polymerase III subunit beta

O: DNA polymerase III subunit beta

P: DNA polymerase III subunit beta

hetero molecules

Summary:

• 692 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	692,244	18
Polymers	692,196	16
Non-polymers	49	2
Water	4,414	245

1

A: DNA polymerase III subunit beta

B: DNA polymerase III subunit beta

Summary:

• defined by author
• Evidence: gel filtration
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,524	2
Polymers	86,524	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

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

2

C: DNA polymerase III subunit beta

D: DNA polymerase III subunit beta

hetero molecules

Summary:

• defined by author
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,549	3
Polymers	86,524	2
Non-polymers	24	1
Water	36	2

Symmetry operations:

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

3

E: DNA polymerase III subunit beta

F: DNA polymerase III subunit beta

Summary:

• defined by author
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,524	2
Polymers	86,524	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

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

4

G: DNA polymerase III subunit beta

H: DNA polymerase III subunit beta

Summary:

• defined by author
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,524	2
Polymers	86,524	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

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

5

I: DNA polymerase III subunit beta

J: DNA polymerase III subunit beta

hetero molecules

Summary:

• defined by author
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,549	3
Polymers	86,524	2
Non-polymers	24	1
Water	36	2

Symmetry operations:

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

6

K: DNA polymerase III subunit beta

L: DNA polymerase III subunit beta

Summary:

• defined by author
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,524	2
Polymers	86,524	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

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

7

M: DNA polymerase III subunit beta

N: DNA polymerase III subunit beta

Summary:

• defined by author
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,524	2
Polymers	86,524	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

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

8

O: DNA polymerase III subunit beta

P: DNA polymerase III subunit beta

Summary:

• defined by author
• 86.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	86,524	2
Polymers	86,524	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

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

Unit cell

Length a, b, c (Å)	72.713, 328.597, 147.497
Angle α, β, γ (deg.)	90.000, 91.530, 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	B
2	16	C
1	17	B
2	17	D
1	18	B
2	18	E
1	19	B
2	19	F
1	20	B
2	20	G
1	21	B
2	21	H
1	22	B
2	22	I
1	23	B
2	23	J
1	24	B
2	24	K
1	25	B
2	25	L
1	26	B
2	26	M
1	27	B
2	27	N
1	28	B
2	28	O
1	29	B
2	29	P
1	30	C
2	30	D
1	31	C
2	31	E
1	32	C
2	32	F
1	33	C
2	33	G
1	34	C
2	34	H
1	35	C
2	35	I
1	36	C
2	36	J
1	37	C
2	37	K
1	38	C
2	38	L
1	39	C
2	39	M
1	40	C
2	40	N
1	41	C
2	41	O
1	42	C
2	42	P
1	43	D
2	43	E
1	44	D
2	44	F
1	45	D
2	45	G
1	46	D
2	46	H
1	47	D
2	47	I
1	48	D
2	48	J
1	49	D
2	49	K
1	50	D
2	50	L
1	51	D
2	51	M
1	52	D
2	52	N
1	53	D
2	53	O
1	54	D
2	54	P
1	55	E
2	55	F
1	56	E
2	56	G
1	57	E
2	57	H
1	58	E
2	58	I
1	59	E
2	59	J
1	60	E
2	60	K
1	61	E
2	61	L
1	62	E
2	62	M
1	63	E
2	63	N
1	64	E
2	64	O
1	65	E
2	65	P
1	66	F
2	66	G
1	67	F
2	67	H
1	68	F
2	68	I
1	69	F
2	69	J
1	70	F
2	70	K
1	71	F
2	71	L
1	72	F
2	72	M
1	73	F
2	73	N
1	74	F
2	74	O
1	75	F
2	75	P
1	76	G
2	76	H
1	77	G
2	77	I
1	78	G
2	78	J
1	79	G
2	79	K
1	80	G
2	80	L
1	81	G
2	81	M
1	82	G
2	82	N
1	83	G
2	83	O
1	84	G
2	84	P
1	85	H
2	85	I
1	86	H
2	86	J
1	87	H
2	87	K
1	88	H
2	88	L
1	89	H
2	89	M
1	90	H
2	90	N
1	91	H
2	91	O
1	92	H
2	92	P
1	93	I
2	93	J
1	94	I
2	94	K
1	95	I
2	95	L
1	96	I
2	96	M
1	97	I
2	97	N
1	98	I
2	98	O
1	99	I
2	99	P
1	100	J
2	100	K
1	101	J
2	101	L
1	102	J
2	102	M
1	103	J
2	103	N
1	104	J
2	104	O
1	105	J
2	105	P
1	106	K
2	106	L
1	107	K
2	107	M
1	108	K
2	108	N
1	109	K
2	109	O
1	110	K
2	110	P
1	111	L
2	111	M
1	112	L
2	112	N
1	113	L
2	113	O
1	114	L
2	114	P
1	115	M
2	115	N
1	116	M
2	116	O
1	117	M
2	117	P
1	118	N
2	118	O
1	119	N
2	119	P
1	120	O
2	120	P

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	0 - 380
2	0	1	0	B	0 - 380
1	0	2	0	A	0 - 379
2	0	2	0	C	0 - 379
1	0	3	0	A	0 - 381
2	0	3	0	D	0 - 381
1	0	4	0	A	0 - 380
2	0	4	0	E	0 - 380
1	0	5	0	A	0 - 380
2	0	5	0	F	0 - 380
1	0	6	0	A	0 - 381
2	0	6	0	G	0 - 381
1	0	7	0	A	0 - 381
2	0	7	0	H	0 - 381
1	0	8	0	A	0 - 381
2	0	8	0	I	0 - 381
1	0	9	0	A	0 - 381
2	0	9	0	J	0 - 381
1	0	10	0	A	1 - 381
2	0	10	0	K	1 - 381
1	0	11	0	A	0 - 381
2	0	11	0	L	0 - 381
1	0	12	0	A	0 - 381
2	0	12	0	M	0 - 381
1	0	13	0	A	0 - 381
2	0	13	0	N	0 - 381
1	0	14	0	A	0 - 381
2	0	14	0	O	0 - 381
1	0	15	0	A	0 - 380
2	0	15	0	P	0 - 380
1	0	16	0	B	-1 - 380
2	0	16	0	C	-1 - 380
1	0	17	0	B	0 - 380
2	0	17	0	D	0 - 380
1	0	18	0	B	0 - 379
2	0	18	0	E	0 - 379
1	0	19	0	B	0 - 380
2	0	19	0	F	0 - 380
1	0	20	0	B	0 - 380
2	0	20	0	G	0 - 380
1	0	21	0	B	-1 - 380
2	0	21	0	H	-1 - 380
1	0	22	0	B	0 - 380
2	0	22	0	I	0 - 380
1	0	23	0	B	-1 - 379
2	0	23	0	J	-1 - 379
1	0	24	0	B	1 - 380
2	0	24	0	K	1 - 380
1	0	25	0	B	-1 - 380
2	0	25	0	L	-1 - 380
1	0	26	0	B	-1 - 380
2	0	26	0	M	-1 - 380
1	0	27	0	B	-1 - 380
2	0	27	0	N	-1 - 380
1	0	28	0	B	0 - 380
2	0	28	0	O	0 - 380
1	0	29	0	B	0 - 380
2	0	29	0	P	0 - 380
1	0	30	0	C	0 - 380
2	0	30	0	D	0 - 380
1	0	31	0	C	0 - 380
2	0	31	0	E	0 - 380
1	0	32	0	C	0 - 380
2	0	32	0	F	0 - 380
1	0	33	0	C	0 - 379
2	0	33	0	G	0 - 379
1	0	34	0	C	-1 - 380
2	0	34	0	H	-1 - 380
1	0	35	0	C	0 - 380
2	0	35	0	I	0 - 380
1	0	36	0	C	-1 - 380
2	0	36	0	J	-1 - 380
1	0	37	0	C	1 - 380
2	0	37	0	K	1 - 380
1	0	38	0	C	-1 - 380
2	0	38	0	L	-1 - 380
1	0	39	0	C	-1 - 380
2	0	39	0	M	-1 - 380
1	0	40	0	C	-1 - 380
2	0	40	0	N	-1 - 380
1	0	41	0	C	0 - 380
2	0	41	0	O	0 - 380
1	0	42	0	C	0 - 380
2	0	42	0	P	0 - 380
1	0	43	0	D	0 - 380
2	0	43	0	E	0 - 380
1	0	44	0	D	0 - 379
2	0	44	0	F	0 - 379
1	0	45	0	D	0 - 381
2	0	45	0	G	0 - 381
1	0	46	0	D	0 - 381
2	0	46	0	H	0 - 381
1	0	47	0	D	0 - 381
2	0	47	0	I	0 - 381
1	0	48	0	D	0 - 381
2	0	48	0	J	0 - 381
1	0	49	0	D	1 - 381
2	0	49	0	K	1 - 381
1	0	50	0	D	0 - 381
2	0	50	0	L	0 - 381
1	0	51	0	D	0 - 381
2	0	51	0	M	0 - 381
1	0	52	0	D	0 - 381
2	0	52	0	N	0 - 381
1	0	53	0	D	0 - 381
2	0	53	0	O	0 - 381
1	0	54	0	D	0 - 380
2	0	54	0	P	0 - 380
1	0	55	0	E	0 - 380
2	0	55	0	F	0 - 380
1	0	56	0	E	0 - 380
2	0	56	0	G	0 - 380
1	0	57	0	E	0 - 379
2	0	57	0	H	0 - 379
1	0	58	0	E	0 - 380
2	0	58	0	I	0 - 380
1	0	59	0	E	0 - 379
2	0	59	0	J	0 - 379
1	0	60	0	E	1 - 380
2	0	60	0	K	1 - 380
1	0	61	0	E	0 - 380
2	0	61	0	L	0 - 380
1	0	62	0	E	0 - 380
2	0	62	0	M	0 - 380
1	0	63	0	E	0 - 380
2	0	63	0	N	0 - 380
1	0	64	0	E	0 - 380
2	0	64	0	O	0 - 380
1	0	65	0	E	0 - 380
2	0	65	0	P	0 - 380
1	0	66	0	F	0 - 380
2	0	66	0	G	0 - 380
1	0	67	0	F	0 - 380
2	0	67	0	H	0 - 380
1	0	68	0	F	0 - 380
2	0	68	0	I	0 - 380
1	0	69	0	F	0 - 379
2	0	69	0	J	0 - 379
1	0	70	0	F	1 - 380
2	0	70	0	K	1 - 380
1	0	71	0	F	0 - 380
2	0	71	0	L	0 - 380
1	0	72	0	F	0 - 380
2	0	72	0	M	0 - 380
1	0	73	0	F	0 - 380
2	0	73	0	N	0 - 380
1	0	74	0	F	0 - 380
2	0	74	0	O	0 - 380
1	0	75	0	F	0 - 380
2	0	75	0	P	0 - 380
1	0	76	0	G	0 - 381
2	0	76	0	H	0 - 381
1	0	77	0	G	0 - 381
2	0	77	0	I	0 - 381
1	0	78	0	G	0 - 381
2	0	78	0	J	0 - 381
1	0	79	0	G	1 - 381
2	0	79	0	K	1 - 381
1	0	80	0	G	0 - 381
2	0	80	0	L	0 - 381
1	0	81	0	G	0 - 381
2	0	81	0	M	0 - 381
1	0	82	0	G	0 - 381
2	0	82	0	N	0 - 381
1	0	83	0	G	0 - 381
2	0	83	0	O	0 - 381
1	0	84	0	G	0 - 380
2	0	84	0	P	0 - 380
1	0	85	0	H	0 - 381
2	0	85	0	I	0 - 381
1	0	86	0	H	-1 - 381
2	0	86	0	J	-1 - 381
1	0	87	0	H	1 - 381
2	0	87	0	K	1 - 381
1	0	88	0	H	-1 - 381
2	0	88	0	L	-1 - 381
1	0	89	0	H	-1 - 381
2	0	89	0	M	-1 - 381
1	0	90	0	H	-1 - 381
2	0	90	0	N	-1 - 381
1	0	91	0	H	0 - 381
2	0	91	0	O	0 - 381
1	0	92	0	H	0 - 380
2	0	92	0	P	0 - 380
1	0	93	0	I	0 - 381
2	0	93	0	J	0 - 381
1	0	94	0	I	1 - 381
2	0	94	0	K	1 - 381
1	0	95	0	I	0 - 381
2	0	95	0	L	0 - 381
1	0	96	0	I	0 - 381
2	0	96	0	M	0 - 381
1	0	97	0	I	0 - 381
2	0	97	0	N	0 - 381
1	0	98	0	I	0 - 381
2	0	98	0	O	0 - 381
1	0	99	0	I	0 - 380
2	0	99	0	P	0 - 380
1	0	100	0	J	1 - 381
2	0	100	0	K	1 - 381
1	0	101	0	J	-1 - 381
2	0	101	0	L	-1 - 381
1	0	102	0	J	-1 - 381
2	0	102	0	M	-1 - 381
1	0	103	0	J	-1 - 381
2	0	103	0	N	-1 - 381
1	0	104	0	J	0 - 381
2	0	104	0	O	0 - 381
1	0	105	0	J	0 - 380
2	0	105	0	P	0 - 380
1	0	106	0	K	1 - 381
2	0	106	0	L	1 - 381
1	0	107	0	K	1 - 381
2	0	107	0	M	1 - 381
1	0	108	0	K	1 - 381
2	0	108	0	N	1 - 381
1	0	109	0	K	1 - 381
2	0	109	0	O	1 - 381
1	0	110	0	K	1 - 380
2	0	110	0	P	1 - 380
1	0	111	0	L	-1 - 381
2	0	111	0	M	-1 - 381
1	0	112	0	L	-1 - 381
2	0	112	0	N	-1 - 381
1	0	113	0	L	0 - 381
2	0	113	0	O	0 - 381
1	0	114	0	L	0 - 380
2	0	114	0	P	0 - 380
1	0	115	0	M	-1 - 381
2	0	115	0	N	-1 - 381
1	0	116	0	M	0 - 381
2	0	116	0	O	0 - 381
1	0	117	0	M	0 - 380
2	0	117	0	P	0 - 380
1	0	118	0	N	0 - 381
2	0	118	0	O	0 - 381
1	0	119	0	N	0 - 380
2	0	119	0	P	0 - 380
1	0	120	0	O	0 - 380
2	0	120	0	P	0 - 380

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

Components

#1: Protein

A B C D E F G H I J K L M N O P
DNA polymerase III subunit beta

Details:

Mass: 43262.219 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: dnaN, A7M79_16225, A7M90_19325, A7N09_15145, AB895_1514, ABUW_0002, APD06_07570, APD31_16715, AZE33_00010, B4R90_12040, B9X95_11540, BGC29_18735, BWP00_10155, CAS83_08665, CBI29_00019, CEB38_18810, IX87_14440, LV38_03508
Cell line (production host): BL21 (DE3) pLysS / Production host: Escherichia coli (E. coli) / References: UniProt: V5V7W3

#2: Chemical

C-401 J-401 ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.54 ų/Da / Density % sol: 51.67 %
• Crystal grow: Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.6 ; Details: 0.1 M Tris-HCl pH 7.6, 0.1 M MgCl2, 7.5%(w/v) PEG 3350, 1% (v/v) DMSO

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.71073 Å
• Detector: Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2013
• Radiation: Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.71073 Å / Relative weight: 1
• Reflection: Resolution: 2.95→164.3 Å / Num. obs: 144290 / % possible obs: 99.8 % / Redundancy: 4.6 % / R_merge(I) obs: 0.115 / R_pim(I) all: 0.059 / R_rim(I) all: 0.13 / Χ²: 0.915 / Net I/σ(I): 8.4 / Num. measured all: 670605

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	Χ2	% possible all
2.95-3.06	4.6	0.602	14388	0.786	0.315	0.681	0.806	99.9
3.06-3.18	4.6	0.441	14451	0.874	0.23	0.498	0.873	99.9
3.18-3.32	4.6	0.315	14411	0.924	0.164	0.357	0.932	99.9
3.32-3.5	4.6	0.23	14381	0.956	0.119	0.26	0.939	99.9
3.5-3.72	4.7	0.173	14405	0.97	0.089	0.195	0.962	99.9
3.72-4	4.7	0.134	14439	0.979	0.069	0.151	0.953	99.9
4-4.41	4.7	0.102	14404	0.986	0.052	0.115	0.924	99.8
4.41-5.04	4.7	0.092	14454	0.987	0.046	0.103	0.988	99.9
5.04-6.35	4.7	0.096	14475	0.984	0.048	0.108	0.908	99.8
6.35-50	4.6	0.047	14482	0.995	0.024	0.053	0.862	99.3

Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
SCALEPACK		data scaling
PHASER		phasing
HKL-2000		data processing
DENZO		data reduction

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K3S

4k3s

Resolution: 2.95→164.3 Å / Cor.coef. F_o:F_c: 0.873 / Cor.coef. F_o:F_c free: 0.83 / SU B: 23.217 / SU ML: 0.425 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.535 / 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	0.2867	6719	5 %	RANDOM
Rwork	0.2484	-	-	-
obs	0.2503	127602	92.48 %	-

• 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 max: 165.85 Ų / B_iso mean: 56.624 Ų / B_iso min: 2.3 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.01 Å2	0 Å2	0.01 Å2
2-	-	0 Å2	0 Å2
3-	-	-	-0.01 Å2

Refinement step

Cycle: final / Resolution: 2.95→164.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	46525	0	2	245	46772
Biso mean	-	-	30	27.94	-
Num. residues	-	-	-	-	6002

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	47096
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	45097
X-RAY DIFFRACTION	r_angle_refined_deg	2.522	1.981	63828
X-RAY DIFFRACTION	r_angle_other_deg	1.374	3	104564
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.935	5	5953
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.514	25.072	2153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.795	15	8640
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.283	15	346
X-RAY DIFFRACTION	r_chiral_restr	0.192	0.2	7800
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	51917
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	8537

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	20708	0.14
1	2	B	20708	0.14
2	1	A	20632	0.14
2	2	C	20632	0.14
3	1	A	20898	0.14
3	2	D	20898	0.14
4	1	A	21122	0.13
4	2	E	21122	0.13
5	1	A	20850	0.14
5	2	F	20850	0.14
6	1	A	20888	0.13
6	2	G	20888	0.13
7	1	A	20884	0.14
7	2	H	20884	0.14
8	1	A	20628	0.13
8	2	I	20628	0.13
9	1	A	20890	0.14
9	2	J	20890	0.14
10	1	A	19698	0.15
10	2	K	19698	0.15
11	1	A	18248	0.15
11	2	L	18248	0.15
12	1	A	20766	0.14
12	2	M	20766	0.14
13	1	A	20614	0.13
13	2	N	20614	0.13
14	1	A	19120	0.15
14	2	O	19120	0.15
15	1	A	20434	0.15
15	2	P	20434	0.15
16	1	B	20576	0.15
16	2	C	20576	0.15
17	1	B	21032	0.14
17	2	D	21032	0.14
18	1	B	21084	0.13
18	2	E	21084	0.13
19	1	B	20856	0.14
19	2	F	20856	0.14
20	1	B	20732	0.14
20	2	G	20732	0.14
21	1	B	20926	0.14
21	2	H	20926	0.14
22	1	B	20290	0.14
22	2	I	20290	0.14
23	1	B	20812	0.14
23	2	J	20812	0.14
24	1	B	19430	0.15
24	2	K	19430	0.15
25	1	B	18508	0.15
25	2	L	18508	0.15
26	1	B	20588	0.15
26	2	M	20588	0.15
27	1	B	20278	0.14
27	2	N	20278	0.14
28	1	B	18944	0.16
28	2	O	18944	0.16
29	1	B	20468	0.13
29	2	P	20468	0.13
30	1	C	20696	0.14
30	2	D	20696	0.14
31	1	C	20726	0.14
31	2	E	20726	0.14
32	1	C	20618	0.14
32	2	F	20618	0.14
33	1	C	20508	0.14
33	2	G	20508	0.14
34	1	C	20422	0.15
34	2	H	20422	0.15
35	1	C	20146	0.13
35	2	I	20146	0.13
36	1	C	20620	0.14
36	2	J	20620	0.14
37	1	C	19224	0.16
37	2	K	19224	0.16
38	1	C	18256	0.15
38	2	L	18256	0.15
39	1	C	20578	0.14
39	2	M	20578	0.14
40	1	C	20234	0.14
40	2	N	20234	0.14
41	1	C	18796	0.16
41	2	O	18796	0.16
42	1	C	20232	0.15
42	2	P	20232	0.15
43	1	D	21144	0.12
43	2	E	21144	0.12
44	1	D	20866	0.14
44	2	F	20866	0.14
45	1	D	21050	0.13
45	2	G	21050	0.13
46	1	D	20914	0.14
46	2	H	20914	0.14
47	1	D	20532	0.13
47	2	I	20532	0.13
48	1	D	20958	0.14
48	2	J	20958	0.14
49	1	D	19712	0.15
49	2	K	19712	0.15
50	1	D	18530	0.14
50	2	L	18530	0.14
51	1	D	20950	0.14
51	2	M	20950	0.14
52	1	D	20508	0.13
52	2	N	20508	0.13
53	1	D	19056	0.16
53	2	O	19056	0.16
54	1	D	20570	0.14
54	2	P	20570	0.14
55	1	E	21166	0.13
55	2	F	21166	0.13
56	1	E	21258	0.12
56	2	G	21258	0.12
57	1	E	21148	0.13
57	2	H	21148	0.13
58	1	E	20762	0.12
58	2	I	20762	0.12
59	1	E	21114	0.13
59	2	J	21114	0.13
60	1	E	19734	0.14
60	2	K	19734	0.14
61	1	E	18488	0.14
61	2	L	18488	0.14
62	1	E	20820	0.13
62	2	M	20820	0.13
63	1	E	20608	0.13
63	2	N	20608	0.13
64	1	E	19040	0.15
64	2	O	19040	0.15
65	1	E	20760	0.13
65	2	P	20760	0.13
66	1	F	20942	0.13
66	2	G	20942	0.13
67	1	F	21000	0.14
67	2	H	21000	0.14
68	1	F	20446	0.13
68	2	I	20446	0.13
69	1	F	20954	0.13
69	2	J	20954	0.13
70	1	F	19372	0.16
70	2	K	19372	0.16
71	1	F	18360	0.15
71	2	L	18360	0.15
72	1	F	20520	0.15
72	2	M	20520	0.15
73	1	F	20434	0.13
73	2	N	20434	0.13
74	1	F	18944	0.15
74	2	O	18944	0.15
75	1	F	20626	0.14
75	2	P	20626	0.14
76	1	G	20950	0.13
76	2	H	20950	0.13
77	1	G	20538	0.13
77	2	I	20538	0.13
78	1	G	20946	0.13
78	2	J	20946	0.13
79	1	G	19756	0.15
79	2	K	19756	0.15
80	1	G	18348	0.15
80	2	L	18348	0.15
81	1	G	20790	0.13
81	2	M	20790	0.13
82	1	G	20464	0.13
82	2	N	20464	0.13
83	1	G	19224	0.15
83	2	O	19224	0.15
84	1	G	20478	0.14
84	2	P	20478	0.14
85	1	H	20628	0.13
85	2	I	20628	0.13
86	1	H	21114	0.13
86	2	J	21114	0.13
87	1	H	19456	0.15
87	2	K	19456	0.15
88	1	H	18502	0.15
88	2	L	18502	0.15
89	1	H	20722	0.14
89	2	M	20722	0.14
90	1	H	20580	0.13
90	2	N	20580	0.13
91	1	H	18998	0.16
91	2	O	18998	0.16
92	1	H	20572	0.14
92	2	P	20572	0.14
93	1	I	20430	0.13
93	2	J	20430	0.13
94	1	I	19462	0.15
94	2	K	19462	0.15
95	1	I	18140	0.14
95	2	L	18140	0.14
96	1	I	20210	0.14
96	2	M	20210	0.14
97	1	I	20110	0.13
97	2	N	20110	0.13
98	1	I	18992	0.15
98	2	O	18992	0.15
99	1	I	20158	0.13
99	2	P	20158	0.13
100	1	J	19358	0.16
100	2	K	19358	0.16
101	1	J	18638	0.14
101	2	L	18638	0.14
102	1	J	20604	0.14
102	2	M	20604	0.14
103	1	J	20494	0.13
103	2	N	20494	0.13
104	1	J	18938	0.15
104	2	O	18938	0.15
105	1	J	20498	0.13
105	2	P	20498	0.13
106	1	K	16942	0.17
106	2	L	16942	0.17
107	1	K	19480	0.16
107	2	M	19480	0.16
108	1	K	19220	0.15
108	2	N	19220	0.15
109	1	K	18190	0.16
109	2	O	18190	0.16
110	1	K	19168	0.16
110	2	P	19168	0.16
111	1	L	18362	0.14
111	2	M	18362	0.14
112	1	L	18240	0.15
112	2	N	18240	0.15
113	1	L	17288	0.16
113	2	O	17288	0.16
114	1	L	17940	0.15
114	2	P	17940	0.15
115	1	M	20468	0.13
115	2	N	20468	0.13
116	1	M	19026	0.15
116	2	O	19026	0.15
117	1	M	20228	0.14
117	2	P	20228	0.14
118	1	N	19030	0.15
118	2	O	19030	0.15
119	1	N	19964	0.14
119	2	P	19964	0.14
120	1	O	18660	0.16
120	2	P	18660	0.16

LS refinement shell

Resolution: 2.946→3.023 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.387	323	-
Rwork	0.331	6262	-
all	-	6585	-
obs	-	-	61.02 %