PDB-7o49: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Sta...

Basic information

• Entry: Database: PDB / ID: 7o49
• Title: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus
• Components: Penicillin-binding protein 1
• Keywords: HYDROLASE / Cell division / antibiotic resistance / peptidoglycan synthesis / transpeptidase

Function / homology

Function:

penicillin binding / cell wall organization / plasma membrane

Domain/homology:

Alpha-Beta Plaits - #2110 / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta

Component:

: / Penicillin-binding protein 1

• Biological species: Staphylococcus aureus subsp. aureus COL (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 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	Apr 5, 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

hetero molecules

Summary:

• 872 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	872,087	40
Polymers	868,296	12
Non-polymers	3,791	28
Water	901	50

1

A: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,709	3
Polymers	72,358	1
Non-polymers	351	2
Water	18	1

Symmetry operations:

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

2

B: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,709	3
Polymers	72,358	1
Non-polymers	351	2
Water	18	1

Symmetry operations:

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

3

C: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,744	4
Polymers	72,358	1
Non-polymers	386	3
Water	18	1

Symmetry operations:

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

4

D: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,744	4
Polymers	72,358	1
Non-polymers	386	3
Water	18	1

Symmetry operations:

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

5

E: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,744	4
Polymers	72,358	1
Non-polymers	386	3
Water	18	1

Symmetry operations:

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

6

F: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,744	4
Polymers	72,358	1
Non-polymers	386	3
Water	18	1

Symmetry operations:

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

7

G: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,709	3
Polymers	72,358	1
Non-polymers	351	2
Water	18	1

Symmetry operations:

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

8

H: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,744	4
Polymers	72,358	1
Non-polymers	386	3
Water	18	1

Symmetry operations:

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

9

I: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,709	3
Polymers	72,358	1
Non-polymers	351	2
Water	18	1

Symmetry operations:

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

10

J: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,744	4
Polymers	72,358	1
Non-polymers	386	3
Water	18	1

Symmetry operations:

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

11

K: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,393	2
Polymers	72,358	1
Non-polymers	35	1
Water	18	1

Symmetry operations:

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

12

L: Penicillin-binding protein 1

hetero molecules

Summary:

• defined by author
• 72.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,393	2
Polymers	72,358	1
Non-polymers	35	1
Water	18	1

Symmetry operations:

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

Unit cell

Length a, b, c (Å)	311.862, 197.148, 221.596
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	GLY	GLY	A	A	64 - 588	1 - 525
2	2	MET	MET	GLY	GLY	C	C	64 - 588	1 - 525
1	3	MET	MET	GLY	GLY	A	A	64 - 588	1 - 525
2	3	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
1	4	MET	MET	SER	SER	A	A	64 - 590	1 - 527
2	4	MET	MET	SER	SER	E	E	64 - 590	1 - 527
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	GLY	GLY	A	A	64 - 588	1 - 525
2	8	MET	MET	GLY	GLY	I	I	64 - 588	1 - 525
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	MET	MET	LYS	LYS	A	A	64 - 589	1 - 526
2	10	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	11	MET	MET	VAL	VAL	A	A	64 - 587	1 - 524
2	11	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
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	LYS	LYS	B	B	64 - 589	1 - 526
2	13	MET	MET	LYS	LYS	D	D	64 - 589	1 - 526
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	LYS	LYS	B	B	64 - 589	1 - 526
2	15	MET	MET	LYS	LYS	F	F	64 - 589	1 - 526
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	LYS	LYS	B	B	64 - 589	1 - 526
2	18	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
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	MET	MET	LYS	LYS	B	B	64 - 589	1 - 526
2	20	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	21	MET	MET	ASN	ASN	B	B	64 - 586	1 - 523
2	21	MET	MET	ASN	ASN	L	L	64 - 586	1 - 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	LYS	LYS	C	C	64 - 589	1 - 526
2	23	MET	MET	LYS	LYS	E	E	64 - 589	1 - 526
1	24	MET	MET	LYS	LYS	C	C	64 - 589	1 - 526
2	24	MET	MET	LYS	LYS	F	F	64 - 589	1 - 526
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	MET	MET	LYS	LYS	C	C	64 - 589	1 - 526
2	29	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	30	MET	MET	VAL	VAL	C	C	64 - 587	1 - 524
2	30	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
1	31	MET	MET	GLY	GLY	D	D	64 - 588	1 - 525
2	31	MET	MET	GLY	GLY	E	E	64 - 588	1 - 525
1	32	MET	MET	LYS	LYS	D	D	64 - 589	1 - 526
2	32	MET	MET	LYS	LYS	F	F	64 - 589	1 - 526
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	LYS	LYS	D	D	64 - 589	1 - 526
2	37	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	38	MET	MET	VAL	VAL	D	D	64 - 587	1 - 524
2	38	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
1	39	MET	MET	SER	SER	E	E	64 - 590	1 - 527
2	39	MET	MET	SER	SER	F	F	64 - 590	1 - 527
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	LYS	LYS	E	E	64 - 589	1 - 526
2	42	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
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	MET	MET	LYS	LYS	E	E	64 - 589	1 - 526
2	44	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	45	MET	MET	VAL	VAL	E	E	64 - 587	1 - 524
2	45	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
1	46	MET	MET	LYS	LYS	F	F	64 - 589	1 - 526
2	46	MET	MET	LYS	LYS	G	G	64 - 589	1 - 526
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	LYS	LYS	F	F	64 - 589	1 - 526
2	48	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
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	MET	MET	LYS	LYS	F	F	64 - 589	1 - 526
2	50	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	51	MET	MET	ASN	ASN	F	F	64 - 586	1 - 523
2	51	MET	MET	ASN	ASN	L	L	64 - 586	1 - 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	MET	MET	LYS	LYS	G	G	64 - 589	1 - 526
2	55	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	56	MET	MET	VAL	VAL	G	G	64 - 587	1 - 524
2	56	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
1	57	MET	MET	GLY	GLY	H	H	64 - 588	1 - 525
2	57	THR	THR	GLY	GLY	I	I	109 - 588	46 - 525
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	ASN	ASN	H	H	64 - 586	1 - 523
2	60	MET	MET	ASN	ASN	L	L	64 - 586	1 - 523
1	61	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
2	61	MET	MET	LYS	LYS	J	J	64 - 589	1 - 526
1	62	MET	MET	LYS	LYS	I	I	64 - 589	1 - 526
2	62	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	63	MET	MET	VAL	VAL	I	I	64 - 587	1 - 524
2	63	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
1	64	MET	MET	LYS	LYS	J	J	64 - 589	1 - 526
2	64	MET	MET	LYS	LYS	K	K	64 - 589	1 - 526
1	65	MET	MET	VAL	VAL	J	J	64 - 587	1 - 524
2	65	MET	MET	VAL	VAL	L	L	64 - 587	1 - 524
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 subsp. aureus COL (bacteria)
Gene: pbp1, SACOL1194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WVW5

#2: Chemical

A-801 B-801 C-801 D-801 E-801 F-801 G-801 H-801 I-801 J-801
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES

Details:

Mass: 238.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM

#3: Chemical

A-802 B-802 C-803 D-803 E-803 F-803 G-802 H-803 I-802 J-803
ChemComp-CD / CADMIUM ION

Details:

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

#4: Chemical

C-802 D-802 E-802 F-802 H-802 J-802 K-801 L-801
ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 50 / 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: 3.92 ų/Da / Density % sol: 68.64 %
• Crystal grow: Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: D,L-malic acid

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2019
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97926 Å / Relative weight: 1
• Reflection: Resolution: 3.03→49.015 Å / Num. obs: 145321 / % possible obs: 89.8 % / Redundancy: 8.9 % / R_merge(I) obs: 0.173 / R_pim(I) all: 0.058 / Net I/σ(I): 11
• Reflection shell: Resolution: 3.033→3.416 Å / R_merge(I) obs: 1.195 / Num. unique obs: 7266 / R_pim(I) all: 0.401

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: 5TRO

5tro

Resolution: 3.03→49 Å / Cor.coef. F_o:F_c: 0.915 / Cor.coef. F_o:F_c free: 0.869 / SU B: 20.443 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.549 / 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	0.2457	7237	5 %	RANDOM
Rwork	0.2111	-	-	-
obs	0.2128	138083	55.24 %	-

• 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: 328.92 Ų / B_iso mean: 93.555 Ų / B_iso min: 17.38 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.01 Å2	-0 Å2	0 Å2
2-	-	1.27 Å2	-0 Å2
3-	-	-	-1.25 Å2

Refinement step

Cycle: final / Resolution: 3.03→49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	48489	0	167	50	48706
Biso mean	-	-	134.53	45.62	-
Num. residues	-	-	-	-	6154

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	49701
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	47437
X-RAY DIFFRACTION	r_angle_refined_deg	1.517	1.65	66852
X-RAY DIFFRACTION	r_angle_other_deg	1.213	1.591	109817
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.115	5	6127
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.676	23.685	2461
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.215	15	9063
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.638	15	210
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	6161
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	56210
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	11258

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	16439	0.1
1	2	B	16439	0.1
2	1	A	16572	0.09
2	2	C	16572	0.09
3	1	A	15743	0.1
3	2	D	15743	0.1
4	1	A	16568	0.09
4	2	E	16568	0.09
5	1	A	16486	0.1
5	2	F	16486	0.1
6	1	A	16569	0.09
6	2	G	16569	0.09
7	1	A	14457	0.1
7	2	H	14457	0.1
8	1	A	16469	0.09
8	2	I	16469	0.09
9	1	A	16512	0.1
9	2	J	16512	0.1
10	1	A	15923	0.1
10	2	K	15923	0.1
11	1	A	15376	0.11
11	2	L	15376	0.11
12	1	B	16423	0.1
12	2	C	16423	0.1
13	1	B	15991	0.1
13	2	D	15991	0.1
14	1	B	16711	0.1
14	2	E	16711	0.1
15	1	B	16790	0.1
15	2	F	16790	0.1
16	1	B	16564	0.1
16	2	G	16564	0.1
17	1	B	14319	0.11
17	2	H	14319	0.11
18	1	B	16559	0.09
18	2	I	16559	0.09
19	1	B	16508	0.1
19	2	J	16508	0.1
20	1	B	16132	0.1
20	2	K	16132	0.1
21	1	B	15467	0.11
21	2	L	15467	0.11
22	1	C	15851	0.1
22	2	D	15851	0.1
23	1	C	16485	0.1
23	2	E	16485	0.1
24	1	C	16462	0.1
24	2	F	16462	0.1
25	1	C	16798	0.08
25	2	G	16798	0.08
26	1	C	14561	0.1
26	2	H	14561	0.1
27	1	C	16627	0.08
27	2	I	16627	0.08
28	1	C	16726	0.09
28	2	J	16726	0.09
29	1	C	16052	0.1
29	2	K	16052	0.1
30	1	C	15500	0.1
30	2	L	15500	0.1
31	1	D	15963	0.09
31	2	E	15963	0.09
32	1	D	15994	0.11
32	2	F	15994	0.11
33	1	D	15764	0.1
33	2	G	15764	0.1
34	1	D	15121	0.09
34	2	H	15121	0.09
35	1	D	15709	0.09
35	2	I	15709	0.09
36	1	D	15834	0.09
36	2	J	15834	0.09
37	1	D	16143	0.1
37	2	K	16143	0.1
38	1	D	15556	0.11
38	2	L	15556	0.11
39	1	E	16764	0.09
39	2	F	16764	0.09
40	1	E	16609	0.09
40	2	G	16609	0.09
41	1	E	14381	0.1
41	2	H	14381	0.1
42	1	E	16497	0.09
42	2	I	16497	0.09
43	1	E	16508	0.1
43	2	J	16508	0.1
44	1	E	16241	0.09
44	2	K	16241	0.09
45	1	E	15555	0.1
45	2	L	15555	0.1
46	1	F	16556	0.09
46	2	G	16556	0.09
47	1	F	14318	0.11
47	2	H	14318	0.11
48	1	F	16413	0.09
48	2	I	16413	0.09
49	1	F	16498	0.1
49	2	J	16498	0.1
50	1	F	16155	0.1
50	2	K	16155	0.1
51	1	F	15564	0.1
51	2	L	15564	0.1
52	1	G	14432	0.1
52	2	H	14432	0.1
53	1	G	16732	0.08
53	2	I	16732	0.08
54	1	G	16653	0.09
54	2	J	16653	0.09
55	1	G	16026	0.1
55	2	K	16026	0.1
56	1	G	15488	0.11
56	2	L	15488	0.11
57	1	H	14418	0.1
57	2	I	14418	0.1
58	1	H	14597	0.1
58	2	J	14597	0.1
59	1	H	15036	0.09
59	2	K	15036	0.09
60	1	H	14840	0.1
60	2	L	14840	0.1
61	1	I	16558	0.09
61	2	J	16558	0.09
62	1	I	15924	0.09
62	2	K	15924	0.09
63	1	I	15411	0.1
63	2	L	15411	0.1
64	1	J	15962	0.1
64	2	K	15962	0.1
65	1	J	15514	0.11
65	2	L	15514	0.11
66	1	K	15706	0.1
66	2	L	15706	0.1

LS refinement shell

Resolution: 3.033→3.112 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.216	1	-
Rwork	0.45	22	-
all	-	23	-
obs	-	-	0.12 %