PDB-7ok9: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Sta...

Basic information

• Entry: Database: PDB / ID: 7ok9
• Title: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with pentaglycine

Components

• Penicillin-binding protein 1
• pentaglycine

• Keywords: HYDROLASE / Cell division / antibiotic resistance / peptidoglycan synthesis / transpeptidase

Function / homology

Function:

penicillin binding / cell wall organization / membrane

Domain/homology:

PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like

Component:

: / Penicillin-binding protein 1

• Biological species: Staphylococcus aureus (bacteria); synthetic construct (others)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å
• Authors: Martinez Caballero, S. / Hermoso, J.A.
• Citation: Journal: Comput Struct Biotechnol J / Year: 2021; Title: Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus , an essential component of the divisome machinery.; Authors: Martinez-Caballero, S. / Mahasenan, K.V. / Kim, C. / Molina, R. / Feltzer, R. / Lee, M. / Bouley, R. / Hesek, D. / Fisher, J.F. / Munoz, I.G. / Chang, M. / Mobashery, S. / Hermoso, J.A.

History

Deposition	May 17, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 3, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _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: Penicillin-binding protein 1

B: Penicillin-binding protein 1

C: Penicillin-binding protein 1

D: Penicillin-binding protein 1

E: Penicillin-binding protein 1

F: Penicillin-binding protein 1

G: Penicillin-binding protein 1

H: Penicillin-binding protein 1

I: Penicillin-binding protein 1

J: Penicillin-binding protein 1

K: Penicillin-binding protein 1

L: Penicillin-binding protein 1

P: pentaglycine

Q: pentaglycine

R: pentaglycine

S: pentaglycine

T: pentaglycine

U: pentaglycine

V: pentaglycine

W: pentaglycine

X: pentaglycine

Y: pentaglycine

hetero molecules

Summary:

• 873 kDa, 22 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	872,559	35
Polymers	871,329	22
Non-polymers	1,230	13
Water	108	6

1

A: Penicillin-binding protein 1

P: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,774	3
Polymers	72,661	2
Non-polymers	112	1
Water	18	1

Symmetry operations:

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

2

B: Penicillin-binding protein 1

R: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,774	3
Polymers	72,661	2
Non-polymers	112	1
Water	18	1

Symmetry operations:

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

3

C: Penicillin-binding protein 1

S: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,774	3
Polymers	72,661	2
Non-polymers	112	1
Water	0

Symmetry operations:

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

4

D: Penicillin-binding protein 1

W: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,809	4
Polymers	72,661	2
Non-polymers	148	2
Water	0

Symmetry operations:

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

5

E: Penicillin-binding protein 1

Q: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,774	3
Polymers	72,661	2
Non-polymers	112	1
Water	0

Symmetry operations:

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

6

F: Penicillin-binding protein 1

X: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,809	4
Polymers	72,661	2
Non-polymers	148	2
Water	18	1

Symmetry operations:

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

7

G: Penicillin-binding protein 1

T: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,774	3
Polymers	72,661	2
Non-polymers	112	1
Water	0

Symmetry operations:

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

8

H: Penicillin-binding protein 1

U: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,809	4
Polymers	72,661	2
Non-polymers	148	2
Water	18	1

Symmetry operations:

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

9

I: Penicillin-binding protein 1

V: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,774	3
Polymers	72,661	2
Non-polymers	112	1
Water	0

Symmetry operations:

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

10

J: Penicillin-binding protein 1

Y: pentaglycine

hetero molecules

Summary:

• defined by author
• 72.8 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,774	3
Polymers	72,661	2
Non-polymers	112	1
Water	18	1

Symmetry operations:

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

11

K: Penicillin-binding protein 1

Summary:

• defined by author
• 72.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,358	1
Polymers	72,358	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

12

L: Penicillin-binding protein 1

Summary:

• defined by author
• 72.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,358	1
Polymers	72,358	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

Unit cell

Length a, b, c (Å)	313.993, 198.186, 220.903
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P21212

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	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
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	MET	MET	SER	SER	A	A	64 - 590	1 - 527
2	1	MET	MET	SER	SER	B	B	64 - 590	1 - 527
1	2	MET	MET	LYS	LYS	A	A	64 - 589	1 - 526
2	2	MET	MET	LYS	LYS	C	C	64 - 589	1 - 526
1	3	MET	MET	LYS	LYS	A	A	64 - 589	1 - 526
2	3	MET	MET	LYS	LYS	D	D	64 - 589	1 - 526
1	4	MET	MET	LYS	LYS	A	A	64 - 591	1 - 528
2	4	MET	MET	LYS	LYS	E	E	64 - 591	1 - 528
1	5	MET	MET	LYS	LYS	A	A	64 - 591	1 - 528
2	5	MET	MET	LYS	LYS	F	F	64 - 591	1 - 528
1	6	MET	MET	GLY	GLY	A	A	64 - 588	1 - 525
2	6	MET	MET	GLY	GLY	G	G	64 - 588	1 - 525
1	7	THR	THR	LYS	LYS	A	A	109 - 589	46 - 526
2	7	MET	MET	LYS	LYS	H	H	64 - 589	1 - 526
1	8	MET	MET	LYS	LYS	A	A	64 - 589	1 - 526
2	8	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
1	9	MET	MET	SER	SER	A	A	64 - 590	1 - 527
2	9	MET	MET	SER	SER	J	J	64 - 590	1 - 527
1	10	THR	THR	VAL	VAL	A	A	109 - 587	46 - 524
2	10	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	11	LYS	LYS	ASN	ASN	A	A	120 - 586	57 - 523
2	11	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	12	MET	MET	LYS	LYS	B	B	64 - 589	1 - 526
2	12	MET	MET	LYS	LYS	C	C	64 - 589	1 - 526
1	13	MET	MET	GLY	GLY	B	B	64 - 588	1 - 525
2	13	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
1	14	MET	MET	SER	SER	B	B	64 - 590	1 - 527
2	14	MET	MET	SER	SER	E	E	64 - 590	1 - 527
1	15	MET	MET	SER	SER	B	B	64 - 590	1 - 527
2	15	MET	MET	SER	SER	F	F	64 - 590	1 - 527
1	16	MET	MET	LYS	LYS	B	B	64 - 589	1 - 526
2	16	MET	MET	LYS	LYS	G	G	64 - 589	1 - 526
1	17	THR	THR	LYS	LYS	B	B	109 - 589	46 - 526
2	17	MET	MET	LYS	LYS	H	H	64 - 589	1 - 526
1	18	MET	MET	SER	SER	B	B	64 - 590	1 - 527
2	18	MET	MET	SER	SER	I	I	64 - 590	1 - 527
1	19	MET	MET	SER	SER	B	B	64 - 590	1 - 527
2	19	MET	MET	SER	SER	J	J	64 - 590	1 - 527
1	20	THR	THR	VAL	VAL	B	B	109 - 587	46 - 524
2	20	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	21	LYS	LYS	ASN	ASN	B	B	120 - 586	57 - 523
2	21	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	22	MET	MET	GLY	GLY	C	C	64 - 588	1 - 525
2	22	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
1	23	MET	MET	GLY	GLY	C	C	64 - 588	1 - 525
2	23	MET	MET	GLY	GLY	E	E	64 - 588	1 - 525
1	24	MET	MET	GLY	GLY	C	C	64 - 588	1 - 525
2	24	MET	MET	GLY	GLY	F	F	64 - 588	1 - 525
1	25	MET	MET	LYS	LYS	C	C	64 - 589	1 - 526
2	25	MET	MET	LYS	LYS	G	G	64 - 589	1 - 526
1	26	THR	THR	GLY	GLY	C	C	109 - 588	46 - 525
2	26	MET	MET	GLY	GLY	H	H	64 - 588	1 - 525
1	27	MET	MET	LYS	LYS	C	C	64 - 589	1 - 526
2	27	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
1	28	MET	MET	LYS	LYS	C	C	64 - 589	1 - 526
2	28	MET	MET	LYS	LYS	J	J	64 - 589	1 - 526
1	29	THR	THR	VAL	VAL	C	C	109 - 587	46 - 524
2	29	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	30	LYS	LYS	ASN	ASN	C	C	120 - 586	57 - 523
2	30	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	31	MET	MET	LYS	LYS	D	D	64 - 589	1 - 526
2	31	MET	MET	LYS	LYS	E	E	64 - 589	1 - 526
1	32	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
2	32	MET	MET	GLY	GLY	F	F	64 - 588	1 - 525
1	33	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
2	33	MET	MET	GLY	GLY	G	G	64 - 588	1 - 525
1	34	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
2	34	MET	MET	GLY	GLY	H	H	64 - 588	1 - 525
1	35	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
2	35	MET	MET	GLY	GLY	I	I	64 - 588	1 - 525
1	36	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
2	36	MET	MET	GLY	GLY	J	J	64 - 588	1 - 525
1	37	MET	MET	VAL	VAL	D	D	64 - 587	1 - 524
2	37	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	38	MET	MET	ASN	ASN	D	D	64 - 586	1 - 523
2	38	MET	MET	ASN	ASN	L	L	64 - 586	1 - 523
1	39	MET	MET	LYS	LYS	E	E	64 - 591	1 - 528
2	39	MET	MET	LYS	LYS	F	F	64 - 591	1 - 528
1	40	MET	MET	LYS	LYS	E	E	64 - 589	1 - 526
2	40	MET	MET	LYS	LYS	G	G	64 - 589	1 - 526
1	41	THR	THR	LYS	LYS	E	E	109 - 589	46 - 526
2	41	MET	MET	LYS	LYS	H	H	64 - 589	1 - 526
1	42	MET	MET	SER	SER	E	E	64 - 590	1 - 527
2	42	MET	MET	SER	SER	I	I	64 - 590	1 - 527
1	43	MET	MET	SER	SER	E	E	64 - 590	1 - 527
2	43	MET	MET	SER	SER	J	J	64 - 590	1 - 527
1	44	THR	THR	VAL	VAL	E	E	109 - 587	46 - 524
2	44	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	45	LYS	LYS	ASN	ASN	E	E	120 - 586	57 - 523
2	45	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	46	MET	MET	GLY	GLY	F	F	64 - 588	1 - 525
2	46	MET	MET	GLY	GLY	G	G	64 - 588	1 - 525
1	47	THR	THR	LYS	LYS	F	F	109 - 589	46 - 526
2	47	MET	MET	LYS	LYS	H	H	64 - 589	1 - 526
1	48	MET	MET	SER	SER	F	F	64 - 590	1 - 527
2	48	MET	MET	SER	SER	I	I	64 - 590	1 - 527
1	49	MET	MET	SER	SER	F	F	64 - 590	1 - 527
2	49	MET	MET	SER	SER	J	J	64 - 590	1 - 527
1	50	THR	THR	VAL	VAL	F	F	109 - 587	46 - 524
2	50	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	51	LYS	LYS	ASN	ASN	F	F	120 - 586	57 - 523
2	51	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	52	THR	THR	GLY	GLY	G	G	109 - 588	46 - 525
2	52	MET	MET	GLY	GLY	H	H	64 - 588	1 - 525
1	53	MET	MET	LYS	LYS	G	G	64 - 589	1 - 526
2	53	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
1	54	MET	MET	LYS	LYS	G	G	64 - 589	1 - 526
2	54	MET	MET	LYS	LYS	J	J	64 - 589	1 - 526
1	55	THR	THR	VAL	VAL	G	G	109 - 587	46 - 524
2	55	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	56	LYS	LYS	ASN	ASN	G	G	120 - 586	57 - 523
2	56	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	57	MET	MET	LYS	LYS	H	H	64 - 589	1 - 526
2	57	THR	THR	LYS	LYS	I	I	109 - 589	46 - 526
1	58	MET	MET	LYS	LYS	H	H	64 - 589	1 - 526
2	58	THR	THR	LYS	LYS	J	J	109 - 589	46 - 526
1	59	MET	MET	GLY	GLY	H	H	64 - 588	1 - 525
2	59	MET	MET	GLY	GLY	K	K	64 - 588	1 - 525
1	60	MET	MET	VAL	VAL	H	H	64 - 587	1 - 524
2	60	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
1	61	MET	MET	SER	SER	I	I	64 - 590	1 - 527
2	61	MET	MET	SER	SER	J	J	64 - 590	1 - 527
1	62	THR	THR	VAL	VAL	I	I	109 - 587	46 - 524
2	62	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	63	LYS	LYS	ASN	ASN	I	I	120 - 586	57 - 523
2	63	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	64	THR	THR	VAL	VAL	J	J	109 - 587	46 - 524
2	64	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
1	65	LYS	LYS	ASN	ASN	J	J	120 - 586	57 - 523
2	65	LYS	LYS	ASN	ASN	L	L	67 - 586	4 - 523
1	66	MET	MET	VAL	VAL	K	K	64 - 587	1 - 524
2	66	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524

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

#1: Protein

A B C D E F G H I J K L
Penicillin-binding protein 1

Details:

Mass: 72358.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria)
Strain: COL / Gene: pbp1, SACOL1194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WVW5

#2: Protein/peptide

P Q R S T U V W X Y
pentaglycine

Details:

Mass: 303.274 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#3: Chemical

A-801 B-801 C-801 D-801 E-801 F-801 G-801 H-801 I-801 J-801
ChemComp-CD / CADMIUM ION

Details:

Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd

#4: Chemical

D-802 F-802 H-802 ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: N

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.96 ų/Da / Density % sol: 68.92 %
• Crystal grow: Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: DL-malic acid

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: Y
• Diffraction source: Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2021
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97926 Å / Relative weight: 1
• Reflection: Resolution: 3.357→49.321 Å / Num. obs: 86448 / % possible obs: 89.1 % / Redundancy: 12.8 % / R_merge(I) obs: 0.674 / R_pim(I) all: 0.195 / Net I/σ(I): 7.5
• Reflection shell: Resolution: 3.357→3.756 Å / R_merge(I) obs: 2.723 / Num. unique obs: 4322 / R_pim(I) all: 0.785
• Serial crystallography sample delivery: Method: fixed target

Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O49

7o49

Resolution: 3.36→49.32 Å / Cor.coef. F_o:F_c: 0.89 / Cor.coef. F_o:F_c free: 0.854 / SU B: 35.962 / SU ML: 0.539 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.915 / 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	0.2669	4313	5 %	RANDOM
Rwork	0.2301	-	-	-
obs	0.232	82133	44.14 %	-

• 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: 371.78 Ų / B_iso mean: 97.202 Ų / B_iso min: 21.57 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	3.02 Å2	0 Å2	-0 Å2
2-	-	2.15 Å2	-0 Å2
3-	-	-	-5.17 Å2

Refinement step

Cycle: final / Resolution: 3.36→49.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	47732	0	178	6	47916
Biso mean	-	-	111.93	39.5	-
Num. residues	-	-	-	-	6059

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	48933
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.018	46604
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.652	65792
X-RAY DIFFRACTION	r_angle_other_deg	1.439	1.597	107804
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.37	5	6024
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.621	23.64	2434
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.965	15	8877
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.743	15	209
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	6059
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	55534
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	11174

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	16589	0.09
1	2	B	16589	0.09
2	1	A	16505	0.1
2	2	C	16505	0.1
3	1	A	15652	0.1
3	2	D	15652	0.1
4	1	A	16587	0.09
4	2	E	16587	0.09
5	1	A	16475	0.1
5	2	F	16475	0.1
6	1	A	16613	0.09
6	2	G	16613	0.09
7	1	A	14307	0.1
7	2	H	14307	0.1
8	1	A	16493	0.1
8	2	I	16493	0.1
9	1	A	16352	0.1
9	2	J	16352	0.1
10	1	A	13793	0.11
10	2	K	13793	0.11
11	1	A	14018	0.11
11	2	L	14018	0.11
12	1	B	16551	0.1
12	2	C	16551	0.1
13	1	B	15921	0.09
13	2	D	15921	0.09
14	1	B	16855	0.09
14	2	E	16855	0.09
15	1	B	16831	0.09
15	2	F	16831	0.09
16	1	B	16695	0.09
16	2	G	16695	0.09
17	1	B	14313	0.1
17	2	H	14313	0.1
18	1	B	16612	0.09
18	2	I	16612	0.09
19	1	B	16425	0.1
19	2	J	16425	0.1
20	1	B	14050	0.12
20	2	K	14050	0.12
21	1	B	14182	0.11
21	2	L	14182	0.11
22	1	C	15760	0.1
22	2	D	15760	0.1
23	1	C	16507	0.11
23	2	E	16507	0.11
24	1	C	16447	0.11
24	2	F	16447	0.11
25	1	C	16655	0.1
25	2	G	16655	0.1
26	1	C	14440	0.1
26	2	H	14440	0.1
27	1	C	16535	0.1
27	2	I	16535	0.1
28	1	C	16414	0.11
28	2	J	16414	0.11
29	1	C	13879	0.12
29	2	K	13879	0.12
30	1	C	14062	0.11
30	2	L	14062	0.11
31	1	D	15855	0.1
31	2	E	15855	0.1
32	1	D	15837	0.1
32	2	F	15837	0.1
33	1	D	15626	0.1
33	2	G	15626	0.1
34	1	D	15013	0.08
34	2	H	15013	0.08
35	1	D	15574	0.1
35	2	I	15574	0.1
36	1	D	15447	0.11
36	2	J	15447	0.11
37	1	D	14747	0.1
37	2	K	14747	0.1
38	1	D	14816	0.1
38	2	L	14816	0.1
39	1	E	16805	0.09
39	2	F	16805	0.09
40	1	E	16688	0.09
40	2	G	16688	0.09
41	1	E	14287	0.1
41	2	H	14287	0.1
42	1	E	16589	0.09
42	2	I	16589	0.09
43	1	E	16394	0.1
43	2	J	16394	0.1
44	1	E	14001	0.12
44	2	K	14001	0.12
45	1	E	14170	0.11
45	2	L	14170	0.11
46	1	F	16541	0.09
46	2	G	16541	0.09
47	1	F	14275	0.11
47	2	H	14275	0.11
48	1	F	16498	0.1
48	2	I	16498	0.1
49	1	F	16347	0.11
49	2	J	16347	0.11
50	1	F	13899	0.12
50	2	K	13899	0.12
51	1	F	14181	0.1
51	2	L	14181	0.1
52	1	G	14281	0.1
52	2	H	14281	0.1
53	1	G	16701	0.08
53	2	I	16701	0.08
54	1	G	16496	0.1
54	2	J	16496	0.1
55	1	G	13787	0.12
55	2	K	13787	0.12
56	1	G	14034	0.11
56	2	L	14034	0.11
57	1	H	14241	0.1
57	2	I	14241	0.1
58	1	H	14151	0.11
58	2	J	14151	0.11
59	1	H	14457	0.1
59	2	K	14457	0.1
60	1	H	14644	0.1
60	2	L	14644	0.1
61	1	I	16503	0.1
61	2	J	16503	0.1
62	1	I	13749	0.12
62	2	K	13749	0.12
63	1	I	13991	0.11
63	2	L	13991	0.11
64	1	J	13691	0.12
64	2	K	13691	0.12
65	1	J	13927	0.11
65	2	L	13927	0.11
66	1	K	14371	0.11
66	2	L	14371	0.11

LS refinement shell

Resolution: 3.36→3.447 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.128	4	-
Rwork	0.404	120	-
all	-	124	-
obs	-	-	0.87 %