PDB-7c6x: Crystal structure of beta-glycosides-binding protein (W41A) of AB...

Basic information

• Entry: Database: PDB / ID: 7c6x
• Title: Crystal structure of beta-glycosides-binding protein (W41A) of ABC transporter in an open state (Form I)
• Components: Sugar ABC transporter, periplasmic sugar-binding protein
• Keywords: SUGAR BINDING PROTEIN / Conformational dynamics / substrate-binding protein / Induced-fit mechanism / Two-step ligand binding / Venus Fly-trap mechanism
• Function / homology: Bacterial extracellular solute-binding protein / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Bacterial extracellular solute-binding protein / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Sugar ABC transporter, periplasmic sugar-binding protein
• Biological species: Thermus thermophilus (bacteria)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
• Authors: Kanaujia, S.P. / Chandravanshi, M. / Samanta, R.

Funding support

India, 1items

Organization	Grant number	Country
Department of Biotechnology (DBT, India)	BT/563/NE/U-Excel/2016	India

• Citation: Journal: J.Mol.Biol. / Year: 2020; Title: Conformational Trapping of a beta-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of ABC Importers.; Authors: Chandravanshi, M. / Samanta, R. / Kanaujia, S.P.

History

Deposition	May 22, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Assembly

Deposited unit

A: Sugar ABC transporter, periplasmic sugar-binding protein

B: Sugar ABC transporter, periplasmic sugar-binding protein

C: Sugar ABC transporter, periplasmic sugar-binding protein

D: Sugar ABC transporter, periplasmic sugar-binding protein

E: Sugar ABC transporter, periplasmic sugar-binding protein

F: Sugar ABC transporter, periplasmic sugar-binding protein

G: Sugar ABC transporter, periplasmic sugar-binding protein

H: Sugar ABC transporter, periplasmic sugar-binding protein

I: Sugar ABC transporter, periplasmic sugar-binding protein

J: Sugar ABC transporter, periplasmic sugar-binding protein

K: Sugar ABC transporter, periplasmic sugar-binding protein

L: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• 552 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	552,375	34
Polymers	550,898	12
Non-polymers	1,477	22
Water	8,719	484

1

A: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 45.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	45,944	2
Polymers	45,908	1
Non-polymers	35	1
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16640 Å2
Method	PISA

2

B: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,050	3
Polymers	45,908	1
Non-polymers	142	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16450 Å2
Method	PISA

3

C: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 45.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	45,944	2
Polymers	45,908	1
Non-polymers	35	1
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16490 Å2
Method	PISA

4

D: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,085	4
Polymers	45,908	1
Non-polymers	177	3
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16480 Å2
Method	PISA

5

E: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,006	3
Polymers	45,908	1
Non-polymers	98	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16490 Å2
Method	PISA

6

F: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,094	3
Polymers	45,908	1
Non-polymers	186	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16440 Å2
Method	PISA

7

G: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,094	3
Polymers	45,908	1
Non-polymers	186	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16750 Å2
Method	PISA

8

H: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	45,979	3
Polymers	45,908	1
Non-polymers	71	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16480 Å2
Method	PISA

9

I: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,050	3
Polymers	45,908	1
Non-polymers	142	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16580 Å2
Method	PISA

10

J: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 45.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	45,944	2
Polymers	45,908	1
Non-polymers	35	1
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16460 Å2
Method	PISA

11

K: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,094	3
Polymers	45,908	1
Non-polymers	186	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16490 Å2
Method	PISA

12

L: Sugar ABC transporter, periplasmic sugar-binding protein

hetero molecules

Summary:

• defined by author&software
• 46.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	46,094	3
Polymers	45,908	1
Non-polymers	186	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	150 Å2
ΔGint	-12 kcal/mol
Surface area	16470 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	80.990, 116.400, 132.140
Angle α, β, γ (deg.)	83.390, 88.730, 89.950
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	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: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

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	LEU	LEU	A	A	3 - 415	4 - 416
2	1	LEU	LEU	B	B	3 - 415	4 - 416
1	2	LEU	LEU	A	A	3 - 415	4 - 416
2	2	LEU	LEU	C	C	3 - 415	4 - 416
1	3	LEU	LEU	A	A	3 - 415	4 - 416
2	3	LEU	LEU	D	D	3 - 415	4 - 416
1	4	LEU	LEU	A	A	3 - 415	4 - 416
2	4	LEU	LEU	E	E	3 - 415	4 - 416
1	5	LEU	LEU	A	A	3 - 415	4 - 416
2	5	LEU	LEU	F	F	3 - 415	4 - 416
1	6	ALA	ALA	A	A	3 - 414	4 - 415
2	6	ALA	ALA	G	G	3 - 414	4 - 415
1	7	LEU	LEU	A	A	3 - 415	4 - 416
2	7	LEU	LEU	H	H	3 - 415	4 - 416
1	8	LEU	LEU	A	A	3 - 415	4 - 416
2	8	LEU	LEU	I	I	3 - 415	4 - 416
1	9	LEU	LEU	A	A	3 - 415	4 - 416
2	9	LEU	LEU	J	J	3 - 415	4 - 416
1	10	LEU	LEU	A	A	3 - 415	4 - 416
2	10	LEU	LEU	K	K	3 - 415	4 - 416
1	11	LEU	LEU	A	A	3 - 415	4 - 416
2	11	LEU	LEU	L	L	3 - 415	4 - 416
1	12	LEU	LEU	B	B	3 - 415	4 - 416
2	12	LEU	LEU	C	C	3 - 415	4 - 416
1	13	LEU	LEU	B	B	3 - 415	4 - 416
2	13	LEU	LEU	D	D	3 - 415	4 - 416
1	14	LEU	LEU	B	B	3 - 415	4 - 416
2	14	LEU	LEU	E	E	3 - 415	4 - 416
1	15	LEU	LEU	B	B	3 - 415	4 - 416
2	15	LEU	LEU	F	F	3 - 415	4 - 416
1	16	ALA	ALA	B	B	3 - 414	4 - 415
2	16	ALA	ALA	G	G	3 - 414	4 - 415
1	17	LEU	LEU	B	B	3 - 415	4 - 416
2	17	LEU	LEU	H	H	3 - 415	4 - 416
1	18	LEU	LEU	B	B	3 - 415	4 - 416
2	18	LEU	LEU	I	I	3 - 415	4 - 416
1	19	LEU	LEU	B	B	3 - 415	4 - 416
2	19	LEU	LEU	J	J	3 - 415	4 - 416
1	20	LEU	LEU	B	B	3 - 415	4 - 416
2	20	LEU	LEU	K	K	3 - 415	4 - 416
1	21	LEU	LEU	B	B	3 - 415	4 - 416
2	21	LEU	LEU	L	L	3 - 415	4 - 416
1	22	LEU	LEU	C	C	3 - 415	4 - 416
2	22	LEU	LEU	D	D	3 - 415	4 - 416
1	23	LEU	LEU	C	C	3 - 415	4 - 416
2	23	LEU	LEU	E	E	3 - 415	4 - 416
1	24	LEU	LEU	C	C	3 - 415	4 - 416
2	24	LEU	LEU	F	F	3 - 415	4 - 416
1	25	ALA	ALA	C	C	3 - 414	4 - 415
2	25	ALA	ALA	G	G	3 - 414	4 - 415
1	26	LEU	LEU	C	C	3 - 415	4 - 416
2	26	LEU	LEU	H	H	3 - 415	4 - 416
1	27	LEU	LEU	C	C	3 - 415	4 - 416
2	27	LEU	LEU	I	I	3 - 415	4 - 416
1	28	LEU	LEU	C	C	3 - 415	4 - 416
2	28	LEU	LEU	J	J	3 - 415	4 - 416
1	29	LEU	LEU	C	C	3 - 415	4 - 416
2	29	LEU	LEU	K	K	3 - 415	4 - 416
1	30	LEU	LEU	C	C	3 - 415	4 - 416
2	30	LEU	LEU	L	L	3 - 415	4 - 416
1	31	LEU	LEU	D	D	3 - 415	4 - 416
2	31	LEU	LEU	E	E	3 - 415	4 - 416
1	32	LEU	LEU	D	D	3 - 415	4 - 416
2	32	LEU	LEU	F	F	3 - 415	4 - 416
1	33	ALA	ALA	D	D	3 - 414	4 - 415
2	33	ALA	ALA	G	G	3 - 414	4 - 415
1	34	LEU	LEU	D	D	3 - 415	4 - 416
2	34	LEU	LEU	H	H	3 - 415	4 - 416
1	35	LEU	LEU	D	D	3 - 415	4 - 416
2	35	LEU	LEU	I	I	3 - 415	4 - 416
1	36	LEU	LEU	D	D	3 - 415	4 - 416
2	36	LEU	LEU	J	J	3 - 415	4 - 416
1	37	LEU	LEU	D	D	3 - 415	4 - 416
2	37	LEU	LEU	K	K	3 - 415	4 - 416
1	38	LEU	LEU	D	D	3 - 415	4 - 416
2	38	LEU	LEU	L	L	3 - 415	4 - 416
1	39	LEU	LEU	E	E	3 - 415	4 - 416
2	39	LEU	LEU	F	F	3 - 415	4 - 416
1	40	ALA	ALA	E	E	3 - 414	4 - 415
2	40	ALA	ALA	G	G	3 - 414	4 - 415
1	41	LEU	LEU	E	E	3 - 415	4 - 416
2	41	LEU	LEU	H	H	3 - 415	4 - 416
1	42	LEU	LEU	E	E	3 - 415	4 - 416
2	42	LEU	LEU	I	I	3 - 415	4 - 416
1	43	LEU	LEU	E	E	3 - 415	4 - 416
2	43	LEU	LEU	J	J	3 - 415	4 - 416
1	44	LEU	LEU	E	E	3 - 415	4 - 416
2	44	LEU	LEU	K	K	3 - 415	4 - 416
1	45	LEU	LEU	E	E	3 - 415	4 - 416
2	45	LEU	LEU	L	L	3 - 415	4 - 416
1	46	ALA	ALA	F	F	3 - 414	4 - 415
2	46	ALA	ALA	G	G	3 - 414	4 - 415
1	47	LEU	LEU	F	F	3 - 415	4 - 416
2	47	LEU	LEU	H	H	3 - 415	4 - 416
1	48	LEU	LEU	F	F	3 - 415	4 - 416
2	48	LEU	LEU	I	I	3 - 415	4 - 416
1	49	LEU	LEU	F	F	3 - 415	4 - 416
2	49	LEU	LEU	J	J	3 - 415	4 - 416
1	50	LEU	LEU	F	F	3 - 415	4 - 416
2	50	LEU	LEU	K	K	3 - 415	4 - 416
1	51	LEU	LEU	F	F	3 - 415	4 - 416
2	51	LEU	LEU	L	L	3 - 415	4 - 416
1	52	ALA	ALA	G	G	3 - 414	4 - 415
2	52	ALA	ALA	H	H	3 - 414	4 - 415
1	53	ALA	ALA	G	G	3 - 414	4 - 415
2	53	ALA	ALA	I	I	3 - 414	4 - 415
1	54	ALA	ALA	G	G	3 - 414	4 - 415
2	54	ALA	ALA	J	J	3 - 414	4 - 415
1	55	ALA	ALA	G	G	3 - 414	4 - 415
2	55	ALA	ALA	K	K	3 - 414	4 - 415
1	56	ALA	ALA	G	G	3 - 414	4 - 415
2	56	ALA	ALA	L	L	3 - 414	4 - 415
1	57	LEU	LEU	H	H	3 - 415	4 - 416
2	57	LEU	LEU	I	I	3 - 415	4 - 416
1	58	LEU	LEU	H	H	3 - 415	4 - 416
2	58	LEU	LEU	J	J	3 - 415	4 - 416
1	59	LEU	LEU	H	H	3 - 415	4 - 416
2	59	LEU	LEU	K	K	3 - 415	4 - 416
1	60	LEU	LEU	H	H	3 - 415	4 - 416
2	60	LEU	LEU	L	L	3 - 415	4 - 416
1	61	LEU	LEU	I	I	3 - 415	4 - 416
2	61	LEU	LEU	J	J	3 - 415	4 - 416
1	62	LEU	LEU	I	I	3 - 415	4 - 416
2	62	LEU	LEU	K	K	3 - 415	4 - 416
1	63	LEU	LEU	I	I	3 - 415	4 - 416
2	63	LEU	LEU	L	L	3 - 415	4 - 416
1	64	LEU	LEU	J	J	3 - 415	4 - 416
2	64	LEU	LEU	K	K	3 - 415	4 - 416
1	65	LEU	LEU	J	J	3 - 415	4 - 416
2	65	LEU	LEU	L	L	3 - 415	4 - 416
1	66	LEU	LEU	K	K	3 - 415	4 - 416
2	66	LEU	LEU	L	L	3 - 415	4 - 416

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
Sugar ABC transporter, periplasmic sugar-binding protein

Details:

Mass: 45908.156 Da / Num. of mol.: 12 / Mutation: W41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHB082 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q53W80

Non-polymers , 5 types, 506 molecules

#2: Chemical

A-501 B-501 C-501 D-501 D-502 E-501 F-501 G-501 H-501 H-502 I-501 J-501 K-501 L-501
ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl

#3: Chemical

B-502 D-503 I-502 ChemComp-PEG / DI(HYDROXYETHYL)ETHER

Details:

Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃

#4: Chemical

E-502 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Chemical

F-502 G-502 K-502 L-502
ChemComp-PGE / TRIETHYLENE GLYCOL

Details:

Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₄

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H₂O

Details

• Has ligand of interest: N
• Has protein modification: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.25 ų/Da / Density % sol: 45.34 % / Description: Triclinic
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium sulphate, 30% PEG 8000

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
• Detector: Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 28, 2019 / Details: VariMax HF
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.5418 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.865
1	1	h,-k,-l	2	0.135

• Reflection: Resolution: 2.65→82.19 Å / Num. obs: 130991 / % possible obs: 94.1 % / Redundancy: 3.5 % / CC_1/2: 0.793 / R_merge(I) obs: 0.264 / R_pim(I) all: 0.16 / R_rim(I) all: 0.309 / Net I/σ(I): 3.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. measured all	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	Net I/σ(I) obs	% possible all
2.65-2.7	3.3	0.432	20071	6096	0.806	0.263	0.507	2	88.3
14.51-82.19	3.9	0.11	3196	830	0.986	0.065	0.128	5.1	97.9

Phasing

• Phasing: Method: molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.65 Å	82.19 Å
Translation	2.65 Å	82.19 Å

Processing

Software

Name	Version	Classification
HKL-3000	3000	data collection
MOSFLM	7.2.2	data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
Coot	0.8.9.2	model building
REFMAC	5.8.0258	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C63

7c63

Resolution: 2.65→82.19 Å / Cor.coef. F_o:F_c: 0.796 / Cor.coef. F_o:F_c free: 0.768 / SU B: 17.625 / SU ML: 0.189 / SU R Cruickshank DPI: 0.0791 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2679	6334	4.8 %	RANDOM
Rwork	0.243	-	-	-
obs	0.2442	124655	88.07 %	-

• 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: 72.67 Ų / B_iso mean: 13.233 Ų / B_iso min: 0.5 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-8.52 Å2	3.33 Å2	3.63 Å2
2-	-	-2.73 Å2	0.71 Å2
3-	-	-	11.24 Å2

Refinement step

Cycle: final / Resolution: 2.65→82.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	37771	0	79	484	38334
Biso mean	-	-	15.89	4.6	-
Num. residues	-	-	-	-	4959

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	38916
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	36028
X-RAY DIFFRACTION	r_angle_refined_deg	1.622	1.639	52979
X-RAY DIFFRACTION	r_angle_other_deg	1.299	1.568	83435
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.375	5	4957
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.614	22.172	1837
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.182	15	5946
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.815	15	221
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	4868
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	44142
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	8437

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	13210	0.05
1	2	B	13210	0.05
2	1	A	13186	0.06
2	2	C	13186	0.06
3	1	A	13310	0.05
3	2	D	13310	0.05
4	1	A	13154	0.06
4	2	E	13154	0.06
5	1	A	13190	0.05
5	2	F	13190	0.05
6	1	A	13146	0.06
6	2	G	13146	0.06
7	1	A	13255	0.05
7	2	H	13255	0.05
8	1	A	13284	0.05
8	2	I	13284	0.05
9	1	A	13068	0.07
9	2	J	13068	0.07
10	1	A	13100	0.06
10	2	K	13100	0.06
11	1	A	13111	0.06
11	2	L	13111	0.06
12	1	B	13372	0.04
12	2	C	13372	0.04
13	1	B	13190	0.05
13	2	D	13190	0.05
14	1	B	13208	0.06
14	2	E	13208	0.06
15	1	B	13366	0.04
15	2	F	13366	0.04
16	1	B	13305	0.05
16	2	G	13305	0.05
17	1	B	13230	0.05
17	2	H	13230	0.05
18	1	B	13206	0.06
18	2	I	13206	0.06
19	1	B	13135	0.06
19	2	J	13135	0.06
20	1	B	13189	0.06
20	2	K	13189	0.06
21	1	B	13171	0.06
21	2	L	13171	0.06
22	1	C	13154	0.06
22	2	D	13154	0.06
23	1	C	13147	0.06
23	2	E	13147	0.06
24	1	C	13340	0.05
24	2	F	13340	0.05
25	1	C	13269	0.05
25	2	G	13269	0.05
26	1	C	13207	0.06
26	2	H	13207	0.06
27	1	C	13177	0.06
27	2	I	13177	0.06
28	1	C	13108	0.06
28	2	J	13108	0.06
29	1	C	13140	0.06
29	2	K	13140	0.06
30	1	C	13127	0.06
30	2	L	13127	0.06
31	1	D	13181	0.06
31	2	E	13181	0.06
32	1	D	13187	0.06
32	2	F	13187	0.06
33	1	D	13144	0.06
33	2	G	13144	0.06
34	1	D	13316	0.05
34	2	H	13316	0.05
35	1	D	13266	0.05
35	2	I	13266	0.05
36	1	D	13076	0.07
36	2	J	13076	0.07
37	1	D	13103	0.06
37	2	K	13103	0.06
38	1	D	13167	0.06
38	2	L	13167	0.06
39	1	E	13224	0.05
39	2	F	13224	0.05
40	1	E	13182	0.06
40	2	G	13182	0.06
41	1	E	13203	0.06
41	2	H	13203	0.06
42	1	E	13171	0.06
42	2	I	13171	0.06
43	1	E	13210	0.06
43	2	J	13210	0.06
44	1	E	13275	0.05
44	2	K	13275	0.05
45	1	E	13313	0.04
45	2	L	13313	0.04
46	1	F	13299	0.05
46	2	G	13299	0.05
47	1	F	13230	0.05
47	2	H	13230	0.05
48	1	F	13208	0.06
48	2	I	13208	0.06
49	1	F	13096	0.06
49	2	J	13096	0.06
50	1	F	13160	0.06
50	2	K	13160	0.06
51	1	F	13191	0.06
51	2	L	13191	0.06
52	1	G	13174	0.06
52	2	H	13174	0.06
53	1	G	13177	0.06
53	2	I	13177	0.06
54	1	G	13091	0.07
54	2	J	13091	0.07
55	1	G	13125	0.06
55	2	K	13125	0.06
56	1	G	13154	0.06
56	2	L	13154	0.06
57	1	H	13293	0.05
57	2	I	13293	0.05
58	1	H	13130	0.07
58	2	J	13130	0.07
59	1	H	13157	0.06
59	2	K	13157	0.06
60	1	H	13202	0.06
60	2	L	13202	0.06
61	1	I	13114	0.07
61	2	J	13114	0.07
62	1	I	13130	0.06
62	2	K	13130	0.06
63	1	I	13153	0.06
63	2	L	13153	0.06
64	1	J	13221	0.06
64	2	K	13221	0.06
65	1	J	13213	0.06
65	2	L	13213	0.06
66	1	K	13259	0.06
66	2	L	13259	0.06

LS refinement shell

Resolution: 2.65→2.66 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.305	80	-
Rwork	0.277	1189	-
all	-	1269	-
obs	-	-	11.59 %

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	0.1823	-0.0457	-0.1336	0.0523	0.0017	0.1347	0.0016	0.0122	-0.0009	-0.0091	0.008	0.0223	-0.0087	0.0051	-0.0097	0.0942	0.0053	-0.0319	0.0606	0.0095	0.0206	-27.1785	-3.2707	0.2442
2	0.2784	-0.0122	0.0748	0.178	-0.0942	0.1923	0.0164	-0.0065	0.0522	-0.0207	-0.0115	-0.0068	-0.0122	0.0041	-0.0049	0.1051	0.0164	-0.023	0.0383	-0.0013	0.0241	-15.1853	25.3405	5.3495
3	0.4172	-0.0591	-0.1767	0.0785	0.0764	0.2548	-0.0141	0.0142	-0.0424	0.0163	0.0054	0.0067	0.0053	-0.0068	0.0086	0.1061	0.0141	-0.0258	0.0296	0.0089	0.0195	16.6453	54.1688	5.3878
4	0.3176	-0.0117	0.0859	0.0237	0.0043	0.2083	-0.0098	0.0425	0.0304	-0.0017	0.0147	-0.0031	0.0017	0.0163	-0.0049	0.1027	0.0026	-0.0367	0.0435	0.0094	0.0191	28.6833	82.824	0.4106
5	0.0093	-0.0103	-0.0159	0.3371	-0.034	0.1616	0.019	-0.0103	-0.0115	0.0101	-0.0159	-0.0204	-0.0201	-0.0086	-0.0032	0.0737	0.0018	-0.0333	0.0602	0.0035	0.043	15.5623	-13.4746	37.9595
6	0.4071	0.0279	-0.2277	0.1576	-0.104	0.2702	-0.0185	0.0184	-0.0429	0.0279	-0.0014	-0.0179	0.0043	0.0012	0.0199	0.1001	-0.0046	-0.0345	0.031	0.0082	0.0221	22.3101	-19.0206	-46.042
7	0.2012	-0.0471	0.1222	0.1166	0.0547	0.1636	-0.0016	0.0008	0.0258	0.0078	-0.0143	0.0055	0.0068	-0.001	0.0159	0.109	-0.0115	-0.0241	0.0445	0.0038	0.0141	-26.7131	68.4918	-45.9185
8	0.2257	-0.0831	-0.1646	0.0507	0.0626	0.1374	-0.0197	-0.0152	-0.0155	0.0058	0.0273	0.0068	-0.011	0.0062	-0.0076	0.1117	0.0019	-0.0138	0.0502	0.0157	0.0329	-14.7109	39.9322	-41.058
9	0.1552	0.0172	0.0959	0.1045	-0.0282	0.1319	-0.0014	-0.0214	0.0182	0.0152	0.008	0.0007	0.0076	-0.0205	-0.0066	0.1082	0.0026	-0.0361	0.0464	0.0076	0.0197	10.2923	9.5475	-40.921
10	0.0127	-0.0528	0.0175	0.4127	0.0454	0.2183	0.0133	-0.0008	-0.0005	0	0.0139	0.0061	0.0055	-0.0095	-0.0272	0.0755	0.0066	-0.0211	0.061	0.0117	0.0385	-14.1015	-23.19	37.9583
11	0.0047	0.0182	-0.0054	0.4495	0.0969	0.248	0.0152	0.0045	-0.005	-0.0204	-0.0045	0.0114	-0.0249	-0.0204	-0.0107	0.0624	0.0133	-0.0218	0.0587	0.0096	0.0368	26.4263	44.7167	52.5911
12	0.0067	0.0184	0.0107	0.2894	-0.0782	0.1378	0.0086	0.0061	0.0007	-0.0075	0.0075	-0.0169	0.0071	0.0013	-0.0161	0.0734	0.0024	-0.0282	0.0706	0.0043	0.0395	-24.9204	34.9994	52.5833

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 415
2	X-RAY DIFFRACTION	2	B	3 - 415
3	X-RAY DIFFRACTION	3	C	3 - 415
4	X-RAY DIFFRACTION	4	D	3 - 415
5	X-RAY DIFFRACTION	5	E	3 - 415
6	X-RAY DIFFRACTION	6	F	3 - 415
7	X-RAY DIFFRACTION	7	G	3 - 418
8	X-RAY DIFFRACTION	8	H	3 - 415
9	X-RAY DIFFRACTION	9	I	3 - 415
10	X-RAY DIFFRACTION	10	J	3 - 415
11	X-RAY DIFFRACTION	11	K	3 - 415
12	X-RAY DIFFRACTION	12	L	3 - 415