PDB-4w4m: Crystal structure of PrgK 19-92

Basic information

• Entry: Database: PDB / ID: 4w4m
• Title: Crystal structure of PrgK 19-92
• Components: Lipoprotein PrgK
• Keywords: PROTEIN TRANSPORT / T3SS / Salmonella

Function / homology

Function:

protein secretion / cell outer membrane

Domain/homology:

Hypothetical protein rpa1041 / Type III secretion system lipoprotein HrcJ/YscJ / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta

Component:

Lipoprotein PrgK

• Biological species: Salmonella typhimurium (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
• Authors: Bergeron, J.R.C. / Strynadka, N.C.J.
• Citation: Journal: Structure / Year: 2015; Title: The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body.; Authors: Julien R C Bergeron / Liam J Worrall / Soumya De / Nikolaos G Sgourakis / Adrienne H Cheung / Emilie Lameignere / Mark Okon / Gregory A Wasney / David Baker / Lawrence P McIntosh / Natalie C J Strynadka / ; Abstract: The type III secretion system (T3SS) is a large macromolecular assembly found at the surface of many pathogenic Gram-negative bacteria. Its role is to inject toxic "effector" proteins into the cells of infected organisms. The molecular details of the assembly of this large, multimembrane-spanning complex remain poorly understood. Here, we report structural, biochemical, and functional analyses of PrgK, an inner-membrane component of the prototypical Salmonella typhimurium T3SS. We have obtained the atomic structures of the two ring building globular domains and show that the C-terminal transmembrane helix is not essential for assembly and secretion. We also demonstrate that structural rearrangement of the two PrgK globular domains, driven by an interconnecting linker region, may promote oligomerization into ring structures. Finally, we used electron microscopy-guided symmetry modeling to propose a structural model for the intimately associated PrgH-PrgK ring interaction within the assembled basal body.

History

Deposition	Aug 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 29, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 14, 2015	Group: Database references
Revision 1.2	Aug 26, 2015	Group: Other
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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: Lipoprotein PrgK

B: Lipoprotein PrgK

C: Lipoprotein PrgK

D: Lipoprotein PrgK

E: Lipoprotein PrgK

F: Lipoprotein PrgK

G: Lipoprotein PrgK

H: Lipoprotein PrgK

I: Lipoprotein PrgK

J: Lipoprotein PrgK

K: Lipoprotein PrgK

L: Lipoprotein PrgK

M: Lipoprotein PrgK

N: Lipoprotein PrgK

Summary:

• 123 kDa, 14 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	122,738	14
Polymers	122,738	14
Non-polymers	0	0
Water	0

1

A: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

2

B: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

3

C: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

4

D: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

5

E: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

6

F: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

7

G: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

8

H: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

9

I: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

10

J: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

11

K: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

12

L: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

13

M: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	1
Non-polymers	0	0
Water	0

Symmetry operations:

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

14

N: Lipoprotein PrgK

Summary:

• defined by author
• 8.77 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	8,767	1
Polymers	8,767	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)	88.120, 112.100, 112.100
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
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	A
2	12	M
1	13	A
2	13	N
1	14	B
2	14	C
1	15	B
2	15	D
1	16	B
2	16	E
1	17	B
2	17	F
1	18	B
2	18	G
1	19	B
2	19	H
1	20	B
2	20	I
1	21	B
2	21	J
1	22	B
2	22	K
1	23	B
2	23	L
1	24	B
2	24	M
1	25	B
2	25	N
1	26	C
2	26	D
1	27	C
2	27	E
1	28	C
2	28	F
1	29	C
2	29	G
1	30	C
2	30	H
1	31	C
2	31	I
1	32	C
2	32	J
1	33	C
2	33	K
1	34	C
2	34	L
1	35	C
2	35	M
1	36	C
2	36	N
1	37	D
2	37	E
1	38	D
2	38	F
1	39	D
2	39	G
1	40	D
2	40	H
1	41	D
2	41	I
1	42	D
2	42	J
1	43	D
2	43	K
1	44	D
2	44	L
1	45	D
2	45	M
1	46	D
2	46	N
1	47	E
2	47	F
1	48	E
2	48	G
1	49	E
2	49	H
1	50	E
2	50	I
1	51	E
2	51	J
1	52	E
2	52	K
1	53	E
2	53	L
1	54	E
2	54	M
1	55	E
2	55	N
1	56	F
2	56	G
1	57	F
2	57	H
1	58	F
2	58	I
1	59	F
2	59	J
1	60	F
2	60	K
1	61	F
2	61	L
1	62	F
2	62	M
1	63	F
2	63	N
1	64	G
2	64	H
1	65	G
2	65	I
1	66	G
2	66	J
1	67	G
2	67	K
1	68	G
2	68	L
1	69	G
2	69	M
1	70	G
2	70	N
1	71	H
2	71	I
1	72	H
2	72	J
1	73	H
2	73	K
1	74	H
2	74	L
1	75	H
2	75	M
1	76	H
2	76	N
1	77	I
2	77	J
1	78	I
2	78	K
1	79	I
2	79	L
1	80	I
2	80	M
1	81	I
2	81	N
1	82	J
2	82	K
1	83	J
2	83	L
1	84	J
2	84	M
1	85	J
2	85	N
1	86	K
2	86	L
1	87	K
2	87	M
1	88	K
2	88	N
1	89	L
2	89	M
1	90	L
2	90	N
1	91	M
2	91	N

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 0

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PRO	PRO	A	A	19 - 79	5 - 65
2	1	PRO	PRO	B	B	19 - 79	5 - 65
1	2	PRO	PRO	A	A	19 - 78	5 - 64
2	2	PRO	PRO	C	C	19 - 78	5 - 64
1	3	PRO	PRO	A	A	19 - 79	5 - 65
2	3	PRO	PRO	D	D	19 - 79	5 - 65
1	4	PRO	PRO	A	A	19 - 78	5 - 64
2	4	PRO	PRO	E	E	19 - 78	5 - 64
1	5	PRO	PRO	A	A	19 - 79	5 - 65
2	5	PRO	PRO	F	F	19 - 79	5 - 65
1	6	PRO	PRO	A	A	19 - 79	5 - 65
2	6	PRO	PRO	G	G	19 - 79	5 - 65
1	7	PRO	PRO	A	A	19 - 78	5 - 64
2	7	PRO	PRO	H	H	19 - 78	5 - 64
1	8	PRO	PRO	A	A	19 - 78	5 - 64
2	8	PRO	PRO	I	I	19 - 78	5 - 64
1	9	PRO	PRO	A	A	19 - 78	5 - 64
2	9	PRO	PRO	J	J	19 - 78	5 - 64
1	10	PRO	PRO	A	A	19 - 78	5 - 64
2	10	PRO	PRO	K	K	19 - 78	5 - 64
1	11	PRO	PRO	A	A	19 - 78	5 - 64
2	11	PRO	PRO	L	L	19 - 78	5 - 64
1	12	PRO	PRO	A	A	19 - 78	5 - 64
2	12	PRO	PRO	M	M	19 - 78	5 - 64
1	13	PRO	PRO	A	A	19 - 78	5 - 64
2	13	PRO	PRO	N	N	19 - 78	5 - 64
1	14	PRO	PRO	B	B	19 - 78	5 - 64
2	14	PRO	PRO	C	C	19 - 78	5 - 64
1	15	PRO	PRO	B	B	19 - 79	5 - 65
2	15	PRO	PRO	D	D	19 - 79	5 - 65
1	16	PRO	PRO	B	B	19 - 78	5 - 64
2	16	PRO	PRO	E	E	19 - 78	5 - 64
1	17	PRO	PRO	B	B	19 - 79	5 - 65
2	17	PRO	PRO	F	F	19 - 79	5 - 65
1	18	PRO	PRO	B	B	19 - 79	5 - 65
2	18	PRO	PRO	G	G	19 - 79	5 - 65
1	19	PRO	PRO	B	B	19 - 78	5 - 64
2	19	PRO	PRO	H	H	19 - 78	5 - 64
1	20	PRO	PRO	B	B	19 - 78	5 - 64
2	20	PRO	PRO	I	I	19 - 78	5 - 64
1	21	PRO	PRO	B	B	19 - 78	5 - 64
2	21	PRO	PRO	J	J	19 - 78	5 - 64
1	22	PRO	PRO	B	B	19 - 78	5 - 64
2	22	PRO	PRO	K	K	19 - 78	5 - 64
1	23	PRO	PRO	B	B	19 - 78	5 - 64
2	23	PRO	PRO	L	L	19 - 78	5 - 64
1	24	PRO	PRO	B	B	19 - 78	5 - 64
2	24	PRO	PRO	M	M	19 - 78	5 - 64
1	25	PRO	PRO	B	B	19 - 78	5 - 64
2	25	PRO	PRO	N	N	19 - 78	5 - 64
1	26	PRO	PRO	C	C	19 - 78	5 - 64
2	26	PRO	PRO	D	D	19 - 78	5 - 64
1	27	ARG	ARG	C	C	19 - 80	5 - 66
2	27	ARG	ARG	E	E	19 - 80	5 - 66
1	28	PRO	PRO	C	C	19 - 78	5 - 64
2	28	PRO	PRO	F	F	19 - 78	5 - 64
1	29	PRO	PRO	C	C	19 - 78	5 - 64
2	29	PRO	PRO	G	G	19 - 78	5 - 64
1	30	PRO	PRO	C	C	19 - 79	5 - 65
2	30	PRO	PRO	H	H	19 - 79	5 - 65
1	31	ARG	ARG	C	C	19 - 80	5 - 66
2	31	ARG	ARG	I	I	19 - 80	5 - 66
1	32	PRO	PRO	C	C	19 - 79	5 - 65
2	32	PRO	PRO	J	J	19 - 79	5 - 65
1	33	PRO	PRO	C	C	19 - 79	5 - 65
2	33	PRO	PRO	K	K	19 - 79	5 - 65
1	34	PRO	PRO	C	C	19 - 79	5 - 65
2	34	PRO	PRO	L	L	19 - 79	5 - 65
1	35	ARG	ARG	C	C	19 - 80	5 - 66
2	35	ARG	ARG	M	M	19 - 80	5 - 66
1	36	PRO	PRO	C	C	19 - 79	5 - 65
2	36	PRO	PRO	N	N	19 - 79	5 - 65
1	37	PRO	PRO	D	D	19 - 78	5 - 64
2	37	PRO	PRO	E	E	19 - 78	5 - 64
1	38	PRO	PRO	D	D	19 - 79	5 - 65
2	38	PRO	PRO	F	F	19 - 79	5 - 65
1	39	PRO	PRO	D	D	19 - 79	5 - 65
2	39	PRO	PRO	G	G	19 - 79	5 - 65
1	40	PRO	PRO	D	D	19 - 78	5 - 64
2	40	PRO	PRO	H	H	19 - 78	5 - 64
1	41	PRO	PRO	D	D	19 - 78	5 - 64
2	41	PRO	PRO	I	I	19 - 78	5 - 64
1	42	PRO	PRO	D	D	19 - 78	5 - 64
2	42	PRO	PRO	J	J	19 - 78	5 - 64
1	43	PRO	PRO	D	D	19 - 78	5 - 64
2	43	PRO	PRO	K	K	19 - 78	5 - 64
1	44	PRO	PRO	D	D	19 - 78	5 - 64
2	44	PRO	PRO	L	L	19 - 78	5 - 64
1	45	PRO	PRO	D	D	19 - 78	5 - 64
2	45	PRO	PRO	M	M	19 - 78	5 - 64
1	46	PRO	PRO	D	D	19 - 78	5 - 64
2	46	PRO	PRO	N	N	19 - 78	5 - 64
1	47	PRO	PRO	E	E	19 - 78	5 - 64
2	47	PRO	PRO	F	F	19 - 78	5 - 64
1	48	PRO	PRO	E	E	19 - 78	5 - 64
2	48	PRO	PRO	G	G	19 - 78	5 - 64
1	49	PRO	PRO	E	E	19 - 79	5 - 65
2	49	PRO	PRO	H	H	19 - 79	5 - 65
1	50	ARG	ARG	E	E	19 - 80	5 - 66
2	50	ARG	ARG	I	I	19 - 80	5 - 66
1	51	PRO	PRO	E	E	19 - 79	5 - 65
2	51	PRO	PRO	J	J	19 - 79	5 - 65
1	52	PRO	PRO	E	E	19 - 79	5 - 65
2	52	PRO	PRO	K	K	19 - 79	5 - 65
1	53	PRO	PRO	E	E	19 - 79	5 - 65
2	53	PRO	PRO	L	L	19 - 79	5 - 65
1	54	ARG	ARG	E	E	19 - 80	5 - 66
2	54	ARG	ARG	M	M	19 - 80	5 - 66
1	55	PRO	PRO	E	E	19 - 79	5 - 65
2	55	PRO	PRO	N	N	19 - 79	5 - 65
1	56	PRO	PRO	F	F	19 - 79	5 - 65
2	56	PRO	PRO	G	G	19 - 79	5 - 65
1	57	PRO	PRO	F	F	19 - 78	5 - 64
2	57	PRO	PRO	H	H	19 - 78	5 - 64
1	58	PRO	PRO	F	F	19 - 78	5 - 64
2	58	PRO	PRO	I	I	19 - 78	5 - 64
1	59	PRO	PRO	F	F	19 - 78	5 - 64
2	59	PRO	PRO	J	J	19 - 78	5 - 64
1	60	PRO	PRO	F	F	19 - 78	5 - 64
2	60	PRO	PRO	K	K	19 - 78	5 - 64
1	61	PRO	PRO	F	F	19 - 78	5 - 64
2	61	PRO	PRO	L	L	19 - 78	5 - 64
1	62	PRO	PRO	F	F	19 - 78	5 - 64
2	62	PRO	PRO	M	M	19 - 78	5 - 64
1	63	PRO	PRO	F	F	19 - 78	5 - 64
2	63	PRO	PRO	N	N	19 - 78	5 - 64
1	64	PRO	PRO	G	G	19 - 78	5 - 64
2	64	PRO	PRO	H	H	19 - 78	5 - 64
1	65	PRO	PRO	G	G	19 - 78	5 - 64
2	65	PRO	PRO	I	I	19 - 78	5 - 64
1	66	PRO	PRO	G	G	19 - 78	5 - 64
2	66	PRO	PRO	J	J	19 - 78	5 - 64
1	67	PRO	PRO	G	G	19 - 78	5 - 64
2	67	PRO	PRO	K	K	19 - 78	5 - 64
1	68	PRO	PRO	G	G	19 - 78	5 - 64
2	68	PRO	PRO	L	L	19 - 78	5 - 64
1	69	PRO	PRO	G	G	19 - 78	5 - 64
2	69	PRO	PRO	M	M	19 - 78	5 - 64
1	70	PRO	PRO	G	G	19 - 78	5 - 64
2	70	PRO	PRO	N	N	19 - 78	5 - 64
1	71	PRO	PRO	H	H	19 - 79	5 - 65
2	71	PRO	PRO	I	I	19 - 79	5 - 65
1	72	ARG	ARG	H	H	19 - 82	5 - 68
2	72	ARG	ARG	J	J	19 - 82	5 - 68
1	73	ARG	ARG	H	H	19 - 82	5 - 68
2	73	ARG	ARG	K	K	19 - 82	5 - 68
1	74	ARG	ARG	H	H	19 - 82	5 - 68
2	74	ARG	ARG	L	L	19 - 82	5 - 68
1	75	PRO	PRO	H	H	19 - 79	5 - 65
2	75	PRO	PRO	M	M	19 - 79	5 - 65
1	76	ARG	ARG	H	H	19 - 80	5 - 66
2	76	ARG	ARG	N	N	19 - 80	5 - 66
1	77	PRO	PRO	I	I	19 - 79	5 - 65
2	77	PRO	PRO	J	J	19 - 79	5 - 65
1	78	PRO	PRO	I	I	19 - 79	5 - 65
2	78	PRO	PRO	K	K	19 - 79	5 - 65
1	79	PRO	PRO	I	I	19 - 79	5 - 65
2	79	PRO	PRO	L	L	19 - 79	5 - 65
1	80	ARG	ARG	I	I	19 - 80	5 - 66
2	80	ARG	ARG	M	M	19 - 80	5 - 66
1	81	PRO	PRO	I	I	19 - 79	5 - 65
2	81	PRO	PRO	N	N	19 - 79	5 - 65
1	82	ARG	ARG	J	J	19 - 82	5 - 68
2	82	ARG	ARG	K	K	19 - 82	5 - 68
1	83	ARG	ARG	J	J	19 - 82	5 - 68
2	83	ARG	ARG	L	L	19 - 82	5 - 68
1	84	PRO	PRO	J	J	19 - 79	5 - 65
2	84	PRO	PRO	M	M	19 - 79	5 - 65
1	85	ARG	ARG	J	J	19 - 80	5 - 66
2	85	ARG	ARG	N	N	19 - 80	5 - 66
1	86	ARG	ARG	K	K	19 - 82	5 - 68
2	86	ARG	ARG	L	L	19 - 82	5 - 68
1	87	PRO	PRO	K	K	19 - 79	5 - 65
2	87	PRO	PRO	M	M	19 - 79	5 - 65
1	88	ARG	ARG	K	K	19 - 80	5 - 66
2	88	ARG	ARG	N	N	19 - 80	5 - 66
1	89	PRO	PRO	L	L	19 - 79	5 - 65
2	89	PRO	PRO	M	M	19 - 79	5 - 65
1	90	ARG	ARG	L	L	19 - 80	5 - 66
2	90	ARG	ARG	N	N	19 - 80	5 - 66
1	91	PRO	PRO	M	M	19 - 79	5 - 65
2	91	PRO	PRO	N	N	19 - 79	5 - 65

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
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Components

#1: Protein

A B C D E F G H I J K L M N
Lipoprotein PrgK

Details:

Mass: 8766.982 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: prgK, STM2871 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P41786

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 2.26 ų/Da / Density % sol: 45.47 %
• Crystal grow: Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 ; Details: 80 mM Phosphate buffer pH 4.0, 20 mM Tris pH 7.0, 25 % PEG 300, 20 mM MgCl2, 20 mM NaCl

Data collection

• Diffraction: Mean temperature: 170 K
• Diffraction source: Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9511 Å
• Detector: Type: RAYONIX MX300HS / Detector: CCD / Date: Jun 20, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9511 Å / Relative weight: 1
• Reflection: Resolution: 3.2→79.39 Å / Num. obs: 17949 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 4.2

Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
iMOSFLM		data reduction
PHASER		phasing
Coot		model building

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→79.39 Å / Cor.coef. F_o:F_c: 0.879 / Cor.coef. F_o:F_c free: 0.839 / SU B: 26.997 / SU ML: 0.448 / Cross valid method: THROUGHOUT / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.27951	975	5.2 %	RANDOM
Rwork	0.24612	-	-	-
obs	0.24783	17949	99.98 %	-

• 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: 42.833 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	4.99 Å2	0 Å2	0 Å2
2-	-	-3.85 Å2	0 Å2
3-	-	-	-1.13 Å2

Refinement step

Cycle: final / Resolution: 3.2→79.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6912	0	0	0	6912

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.02	7043
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	6882
X-RAY DIFFRACTION	r_angle_refined_deg	1.93	1.972	9552
X-RAY DIFFRACTION	r_angle_other_deg	1.996	3	15910
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	17.471	5	858
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.364	26.573	321
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.884	15	1271
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.674	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	1082
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	7868
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1437
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	3576	0.1
1	2	B	3576	0.1
2	1	A	3502	0.12
2	2	C	3502	0.12
3	1	A	3596	0.09
3	2	D	3596	0.09
4	1	A	3520	0.1
4	2	E	3520	0.1
5	1	A	3545	0.11
5	2	F	3545	0.11
6	1	A	3544	0.11
6	2	G	3544	0.11
7	1	A	3576	0.08
7	2	H	3576	0.08
8	1	A	3531	0.1
8	2	I	3531	0.1
9	1	A	3559	0.09
9	2	J	3559	0.09
10	1	A	3516	0.1
10	2	K	3516	0.1
11	1	A	3485	0.11
11	2	L	3485	0.11
12	1	A	3217	0.14
12	2	M	3217	0.14
13	1	A	3502	0.11
13	2	N	3502	0.11
14	1	B	3567	0.12
14	2	C	3567	0.12
15	1	B	3574	0.1
15	2	D	3574	0.1
16	1	B	3515	0.1
16	2	E	3515	0.1
17	1	B	3619	0.1
17	2	F	3619	0.1
18	1	B	3650	0.1
18	2	G	3650	0.1
19	1	B	3554	0.11
19	2	H	3554	0.11
20	1	B	3507	0.12
20	2	I	3507	0.12
21	1	B	3557	0.11
21	2	J	3557	0.11
22	1	B	3611	0.09
22	2	K	3611	0.09
23	1	B	3542	0.11
23	2	L	3542	0.11
24	1	B	3297	0.14
24	2	M	3297	0.14
25	1	B	3522	0.11
25	2	N	3522	0.11
26	1	C	3492	0.11
26	2	D	3492	0.11
27	1	C	3622	0.12
27	2	E	3622	0.12
28	1	C	3554	0.11
28	2	F	3554	0.11
29	1	C	3539	0.12
29	2	G	3539	0.12
30	1	C	3631	0.11
30	2	H	3631	0.11
31	1	C	3638	0.13
31	2	I	3638	0.13
32	1	C	3597	0.12
32	2	J	3597	0.12
33	1	C	3640	0.11
33	2	K	3640	0.11
34	1	C	3611	0.11
34	2	L	3611	0.11
35	1	C	3423	0.14
35	2	M	3423	0.14
36	1	C	3562	0.13
36	2	N	3562	0.13
37	1	D	3545	0.08
37	2	E	3545	0.08
38	1	D	3558	0.1
38	2	F	3558	0.1
39	1	D	3546	0.1
39	2	G	3546	0.1
40	1	D	3592	0.07
40	2	H	3592	0.07
41	1	D	3589	0.09
41	2	I	3589	0.09
42	1	D	3563	0.09
42	2	J	3563	0.09
43	1	D	3501	0.1
43	2	K	3501	0.1
44	1	D	3500	0.09
44	2	L	3500	0.09
45	1	D	3212	0.14
45	2	M	3212	0.14
46	1	D	3513	0.1
46	2	N	3513	0.1
47	1	E	3494	0.1
47	2	F	3494	0.1
48	1	E	3512	0.09
48	2	G	3512	0.09
49	1	E	3649	0.08
49	2	H	3649	0.08
50	1	E	3665	0.11
50	2	I	3665	0.11
51	1	E	3612	0.11
51	2	J	3612	0.11
52	1	E	3578	0.1
52	2	K	3578	0.1
53	1	E	3556	0.11
53	2	L	3556	0.11
54	1	E	3356	0.14
54	2	M	3356	0.14
55	1	E	3602	0.1
55	2	N	3602	0.1
56	1	F	3675	0.07
56	2	G	3675	0.07
57	1	F	3529	0.1
57	2	H	3529	0.1
58	1	F	3506	0.11
58	2	I	3506	0.11
59	1	F	3511	0.12
59	2	J	3511	0.12
60	1	F	3581	0.08
60	2	K	3581	0.08
61	1	F	3507	0.11
61	2	L	3507	0.11
62	1	F	3261	0.14
62	2	M	3261	0.14
63	1	F	3465	0.12
63	2	N	3465	0.12
64	1	G	3525	0.1
64	2	H	3525	0.1
65	1	G	3501	0.11
65	2	I	3501	0.11
66	1	G	3521	0.11
66	2	J	3521	0.11
67	1	G	3587	0.09
67	2	K	3587	0.09
68	1	G	3516	0.11
68	2	L	3516	0.11
69	1	G	3272	0.14
69	2	M	3272	0.14
70	1	G	3469	0.12
70	2	N	3469	0.12
71	1	H	3662	0.08
71	2	I	3662	0.08
72	1	H	3832	0.1
72	2	J	3832	0.1
73	1	H	3772	0.1
73	2	K	3772	0.1
74	1	H	3737	0.11
74	2	L	3737	0.11
75	1	H	3351	0.13
75	2	M	3351	0.13
76	1	H	3710	0.1
76	2	N	3710	0.1
77	1	I	3662	0.09
77	2	J	3662	0.09
78	1	I	3588	0.11
78	2	K	3588	0.11
79	1	I	3605	0.09
79	2	L	3605	0.09
80	1	I	3355	0.14
80	2	M	3355	0.14
81	1	I	3616	0.1
81	2	N	3616	0.1
82	1	J	3808	0.11
82	2	K	3808	0.11
83	1	J	3748	0.11
83	2	L	3748	0.11
84	1	J	3369	0.13
84	2	M	3369	0.13
85	1	J	3706	0.1
85	2	N	3706	0.1
86	1	K	3774	0.11
86	2	L	3774	0.11
87	1	K	3406	0.12
87	2	M	3406	0.12
88	1	K	3636	0.11
88	2	N	3636	0.11
89	1	L	3374	0.13
89	2	M	3374	0.13
90	1	L	3601	0.12
90	2	N	3601	0.12
91	1	M	3303	0.14
91	2	N	3303	0.14

LS refinement shell

Resolution: 3.2→3.283 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.431	80	-
Rwork	0.318	1285	-
obs	-	-	100 %