PDB-5cms: Structural Insights into the Mechanism of Escherichia coli Ymdb

Basic information

• Entry: Database: PDB / ID: 5cms
• Title: Structural Insights into the Mechanism of Escherichia coli Ymdb
• Components: O-acetyl-ADP-ribose deacetylase
• Keywords: HYDROLASE / deacetylase / ADPr / OAADPr / macro domain

Function / homology

Function:

O-acetyl-ADP-ribose deacetylase / negative regulation of ribonuclease activity / regulation of single-species biofilm formation on inanimate substrate / ribonuclease inhibitor activity / O-acetyl-ADP-ribose deacetylase activity / purine nucleoside binding / purine nucleoside metabolic process / deacetylase activity / endoribonuclease inhibitor activity / transferase activity / response to antibiotic / enzyme binding

Domain/homology:

O-acetyl-ADP-ribose deacetylase / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ADENOSINE-5-DIPHOSPHORIBOSE / O-acetyl-ADP-ribose deacetylase / O-acetyl-ADP-ribose deacetylase

• Biological species: Escherichia coli (E. coli)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
• Authors: Zhang, W. / Wang, C. / Song, Y. / Shao, C. / Zhang, X. / Zang, J.
• Citation: Journal: J.Struct.Biol. / Year: 2015; Title: Structural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase; Authors: Zhang, W. / Wang, C. / Song, Y. / Shao, C. / Zhang, X. / Zang, J.

History

Deposition	Jul 17, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2015	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Data collection / Database references / Derived calculations Category: citation / diffrn_detector / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 8, 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

Assembly

Deposited unit

R: O-acetyl-ADP-ribose deacetylase

A: O-acetyl-ADP-ribose deacetylase

B: O-acetyl-ADP-ribose deacetylase

C: O-acetyl-ADP-ribose deacetylase

D: O-acetyl-ADP-ribose deacetylase

E: O-acetyl-ADP-ribose deacetylase

F: O-acetyl-ADP-ribose deacetylase

G: O-acetyl-ADP-ribose deacetylase

H: O-acetyl-ADP-ribose deacetylase

I: O-acetyl-ADP-ribose deacetylase

J: O-acetyl-ADP-ribose deacetylase

K: O-acetyl-ADP-ribose deacetylase

L: O-acetyl-ADP-ribose deacetylase

M: O-acetyl-ADP-ribose deacetylase

N: O-acetyl-ADP-ribose deacetylase

O: O-acetyl-ADP-ribose deacetylase

P: O-acetyl-ADP-ribose deacetylase

Q: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

• 365 kDa, 18 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	365,247	54
Polymers	353,450	18
Non-polymers	11,797	36
Water	2,162	120

1

R: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8030 Å2
Method	PISA

2

A: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	7870 Å2
Method	PISA

3

B: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	190 Å2
ΔGint	-14 kcal/mol
Surface area	8150 Å2
Method	PISA

4

C: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	1030 Å2
ΔGint	-11 kcal/mol
Surface area	7820 Å2
Method	PISA

5

D: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8120 Å2
Method	PISA

6

E: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8090 Å2
Method	PISA

7

F: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8000 Å2
Method	PISA

8

G: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	7890 Å2
Method	PISA

9

H: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	190 Å2
ΔGint	-14 kcal/mol
Surface area	7970 Å2
Method	PISA

10

I: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8030 Å2
Method	PISA

11

J: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	7970 Å2
Method	PISA

12

K: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	7880 Å2
Method	PISA

13

L: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8010 Å2
Method	PISA

14

M: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8120 Å2
Method	PISA

15

N: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	7780 Å2
Method	PISA

16

O: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8090 Å2
Method	PISA

17

P: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	7990 Å2
Method	PISA

18

Q: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,291	3
Polymers	19,636	1
Non-polymers	655	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	8070 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	290.019, 290.019, 114.324
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	R
2	1	A
1	2	R
2	2	B
1	3	R
2	3	C
1	4	R
2	4	D
1	5	R
2	5	E
1	6	R
2	6	F
1	7	R
2	7	G
1	8	R
2	8	H
1	9	R
2	9	I
1	10	R
2	10	J
1	11	R
2	11	K
1	12	R
2	12	L
1	13	R
2	13	M
1	14	R
2	14	N
1	15	R
2	15	O
1	16	R
2	16	P
1	17	R
2	17	Q
1	18	A
2	18	B
1	19	A
2	19	C
1	20	A
2	20	D
1	21	A
2	21	E
1	22	A
2	22	F
1	23	A
2	23	G
1	24	A
2	24	H
1	25	A
2	25	I
1	26	A
2	26	J
1	27	A
2	27	K
1	28	A
2	28	L
1	29	A
2	29	M
1	30	A
2	30	N
1	31	A
2	31	O
1	32	A
2	32	P
1	33	A
2	33	Q
1	34	B
2	34	C
1	35	B
2	35	D
1	36	B
2	36	E
1	37	B
2	37	F
1	38	B
2	38	G
1	39	B
2	39	H
1	40	B
2	40	I
1	41	B
2	41	J
1	42	B
2	42	K
1	43	B
2	43	L
1	44	B
2	44	M
1	45	B
2	45	N
1	46	B
2	46	O
1	47	B
2	47	P
1	48	B
2	48	Q
1	49	C
2	49	D
1	50	C
2	50	E
1	51	C
2	51	F
1	52	C
2	52	G
1	53	C
2	53	H
1	54	C
2	54	I
1	55	C
2	55	J
1	56	C
2	56	K
1	57	C
2	57	L
1	58	C
2	58	M
1	59	C
2	59	N
1	60	C
2	60	O
1	61	C
2	61	P
1	62	C
2	62	Q
1	63	D
2	63	E
1	64	D
2	64	F
1	65	D
2	65	G
1	66	D
2	66	H
1	67	D
2	67	I
1	68	D
2	68	J
1	69	D
2	69	K
1	70	D
2	70	L
1	71	D
2	71	M
1	72	D
2	72	N
1	73	D
2	73	O
1	74	D
2	74	P
1	75	D
2	75	Q
1	76	E
2	76	F
1	77	E
2	77	G
1	78	E
2	78	H
1	79	E
2	79	I
1	80	E
2	80	J
1	81	E
2	81	K
1	82	E
2	82	L
1	83	E
2	83	M
1	84	E
2	84	N
1	85	E
2	85	O
1	86	E
2	86	P
1	87	E
2	87	Q
1	88	F
2	88	G
1	89	F
2	89	H
1	90	F
2	90	I
1	91	F
2	91	J
1	92	F
2	92	K
1	93	F
2	93	L
1	94	F
2	94	M
1	95	F
2	95	N
1	96	F
2	96	O
1	97	F
2	97	P
1	98	F
2	98	Q
1	99	G
2	99	H
1	100	G
2	100	I
1	101	G
2	101	J
1	102	G
2	102	K
1	103	G
2	103	L
1	104	G
2	104	M
1	105	G
2	105	N
1	106	G
2	106	O
1	107	G
2	107	P
1	108	G
2	108	Q
1	109	H
2	109	I
1	110	H
2	110	J
1	111	H
2	111	K
1	112	H
2	112	L
1	113	H
2	113	M
1	114	H
2	114	N
1	115	H
2	115	O
1	116	H
2	116	P
1	117	H
2	117	Q
1	118	I
2	118	J
1	119	I
2	119	K
1	120	I
2	120	L
1	121	I
2	121	M
1	122	I
2	122	N
1	123	I
2	123	O
1	124	I
2	124	P
1	125	I
2	125	Q
1	126	J
2	126	K
1	127	J
2	127	L
1	128	J
2	128	M
1	129	J
2	129	N
1	130	J
2	130	O
1	131	J
2	131	P
1	132	J
2	132	Q
1	133	K
2	133	L
1	134	K
2	134	M
1	135	K
2	135	N
1	136	K
2	136	O
1	137	K
2	137	P
1	138	K
2	138	Q
1	139	L
2	139	M
1	140	L
2	140	N
1	141	L
2	141	O
1	142	L
2	142	P
1	143	L
2	143	Q
1	144	M
2	144	N
1	145	M
2	145	O
1	146	M
2	146	P
1	147	M
2	147	Q
1	148	N
2	148	O
1	149	N
2	149	P
1	150	N
2	150	Q
1	151	O
2	151	P
1	152	O
2	152	Q
1	153	P
2	153	Q

NCS domain segments:

Component-ID: 0 / Refine code: 0

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	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	1	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
1	2	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	2	THR	THR	GLN	GLN	B	C	3 - 173	9 - 179
1	3	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	3	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
1	4	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	4	THR	THR	GLN	GLN	D	E	3 - 173	9 - 179
1	5	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	5	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
1	6	THR	THR	GLN	GLN	R	A	3 - 174	9 - 180
2	6	THR	THR	GLN	GLN	F	G	3 - 174	9 - 180
1	7	THR	THR	THR	THR	R	A	3 - 172	9 - 178
2	7	THR	THR	THR	THR	G	H	3 - 172	9 - 178
1	8	THR	THR	GLN	GLN	R	A	3 - 174	9 - 180
2	8	THR	THR	GLN	GLN	H	I	3 - 174	9 - 180
1	9	THR	THR	THR	THR	R	A	3 - 172	9 - 178
2	9	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	10	THR	THR	GLN	GLN	R	A	3 - 174	9 - 180
2	10	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
1	11	THR	THR	THR	THR	R	A	3 - 172	9 - 178
2	11	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	12	THR	THR	THR	THR	R	A	3 - 172	9 - 178
2	12	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	13	THR	THR	GLN	GLN	R	A	3 - 174	9 - 180
2	13	THR	THR	GLN	GLN	M	N	3 - 174	9 - 180
1	14	THR	THR	THR	THR	R	A	3 - 172	9 - 178
2	14	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	15	THR	THR	GLN	GLN	R	A	3 - 174	9 - 180
2	15	THR	THR	GLN	GLN	O	P	3 - 174	9 - 180
1	16	THR	THR	GLN	GLN	R	A	3 - 174	9 - 180
2	16	THR	THR	GLN	GLN	P	Q	3 - 174	9 - 180
1	17	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	17	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	18	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	18	LYS	LYS	GLN	GLN	B	C	2 - 174	8 - 180
1	19	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	19	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
1	20	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	20	LYS	LYS	GLN	GLN	D	E	2 - 174	8 - 180
1	21	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	21	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
1	22	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
2	22	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
1	23	THR	THR	THR	THR	A	B	3 - 172	9 - 178
2	23	THR	THR	THR	THR	G	H	3 - 172	9 - 178
1	24	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
2	24	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
1	25	THR	THR	THR	THR	A	B	3 - 172	9 - 178
2	25	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	26	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
2	26	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	27	THR	THR	THR	THR	A	B	3 - 172	9 - 178
2	27	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	28	THR	THR	THR	THR	A	B	3 - 172	9 - 178
2	28	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	29	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
2	29	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
1	30	THR	THR	THR	THR	A	B	3 - 172	9 - 178
2	30	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	31	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
2	31	THR	THR	GLN	GLN	O	P	3 - 173	9 - 179
1	32	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
2	32	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
1	33	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	33	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	34	LYS	LYS	GLN	GLN	B	C	2 - 174	8 - 180
2	34	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
1	35	LYS	LYS	GLN	GLN	B	C	2 - 174	8 - 180
2	35	LYS	LYS	GLN	GLN	D	E	2 - 174	8 - 180
1	36	LYS	LYS	GLN	GLN	B	C	2 - 174	8 - 180
2	36	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
1	37	THR	THR	GLN	GLN	B	C	3 - 173	9 - 179
2	37	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
1	38	THR	THR	THR	THR	B	C	3 - 172	9 - 178
2	38	THR	THR	THR	THR	G	H	3 - 172	9 - 178
1	39	THR	THR	GLN	GLN	B	C	3 - 173	9 - 179
2	39	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
1	40	THR	THR	THR	THR	B	C	3 - 172	9 - 178
2	40	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	41	THR	THR	GLN	GLN	B	C	3 - 173	9 - 179
2	41	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	42	THR	THR	THR	THR	B	C	3 - 172	9 - 178
2	42	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	43	THR	THR	THR	THR	B	C	3 - 172	9 - 178
2	43	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	44	THR	THR	GLN	GLN	B	C	3 - 173	9 - 179
2	44	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
1	45	THR	THR	THR	THR	B	C	3 - 172	9 - 178
2	45	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	46	THR	THR	GLN	GLN	B	C	3 - 173	9 - 179
2	46	THR	THR	GLN	GLN	O	P	3 - 173	9 - 179
1	47	THR	THR	GLN	GLN	B	C	3 - 173	9 - 179
2	47	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
1	48	LYS	LYS	GLN	GLN	B	C	2 - 174	8 - 180
2	48	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	49	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	49	LYS	LYS	GLN	GLN	D	E	2 - 174	8 - 180
1	50	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	50	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
1	51	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
2	51	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
1	52	THR	THR	THR	THR	C	D	3 - 172	9 - 178
2	52	THR	THR	THR	THR	G	H	3 - 172	9 - 178
1	53	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
2	53	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
1	54	THR	THR	THR	THR	C	D	3 - 172	9 - 178
2	54	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	55	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
2	55	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	56	THR	THR	THR	THR	C	D	3 - 172	9 - 178
2	56	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	57	THR	THR	THR	THR	C	D	3 - 172	9 - 178
2	57	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	58	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
2	58	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
1	59	THR	THR	THR	THR	C	D	3 - 172	9 - 178
2	59	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	60	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
2	60	THR	THR	GLN	GLN	O	P	3 - 173	9 - 179
1	61	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
2	61	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
1	62	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	62	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	63	LYS	LYS	GLN	GLN	D	E	2 - 174	8 - 180
2	63	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
1	64	THR	THR	GLN	GLN	D	E	3 - 173	9 - 179
2	64	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
1	65	THR	THR	THR	THR	D	E	3 - 172	9 - 178
2	65	THR	THR	THR	THR	G	H	3 - 172	9 - 178
1	66	THR	THR	GLN	GLN	D	E	3 - 173	9 - 179
2	66	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
1	67	THR	THR	THR	THR	D	E	3 - 172	9 - 178
2	67	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	68	THR	THR	GLN	GLN	D	E	3 - 173	9 - 179
2	68	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	69	THR	THR	THR	THR	D	E	3 - 172	9 - 178
2	69	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	70	THR	THR	THR	THR	D	E	3 - 172	9 - 178
2	70	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	71	THR	THR	GLN	GLN	D	E	3 - 173	9 - 179
2	71	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
1	72	THR	THR	THR	THR	D	E	3 - 172	9 - 178
2	72	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	73	THR	THR	GLN	GLN	D	E	3 - 173	9 - 179
2	73	THR	THR	GLN	GLN	O	P	3 - 173	9 - 179
1	74	THR	THR	GLN	GLN	D	E	3 - 173	9 - 179
2	74	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
1	75	LYS	LYS	GLN	GLN	D	E	2 - 174	8 - 180
2	75	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	76	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
2	76	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
1	77	THR	THR	THR	THR	E	F	3 - 172	9 - 178
2	77	THR	THR	THR	THR	G	H	3 - 172	9 - 178
1	78	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
2	78	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
1	79	THR	THR	THR	THR	E	F	3 - 172	9 - 178
2	79	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	80	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
2	80	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	81	THR	THR	THR	THR	E	F	3 - 172	9 - 178
2	81	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	82	THR	THR	THR	THR	E	F	3 - 172	9 - 178
2	82	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	83	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
2	83	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
1	84	THR	THR	THR	THR	E	F	3 - 172	9 - 178
2	84	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	85	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
2	85	THR	THR	GLN	GLN	O	P	3 - 173	9 - 179
1	86	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
2	86	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
1	87	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	87	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	88	THR	THR	THR	THR	F	G	3 - 172	9 - 178
2	88	THR	THR	THR	THR	G	H	3 - 172	9 - 178
1	89	THR	THR	GLN	GLN	F	G	3 - 174	9 - 180
2	89	THR	THR	GLN	GLN	H	I	3 - 174	9 - 180
1	90	THR	THR	THR	THR	F	G	3 - 172	9 - 178
2	90	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	91	THR	THR	GLN	GLN	F	G	3 - 174	9 - 180
2	91	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
1	92	THR	THR	THR	THR	F	G	3 - 172	9 - 178
2	92	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	93	THR	THR	THR	THR	F	G	3 - 172	9 - 178
2	93	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	94	THR	THR	GLN	GLN	F	G	3 - 174	9 - 180
2	94	THR	THR	GLN	GLN	M	N	3 - 174	9 - 180
1	95	THR	THR	THR	THR	F	G	3 - 172	9 - 178
2	95	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	96	THR	THR	GLN	GLN	F	G	3 - 174	9 - 180
2	96	THR	THR	GLN	GLN	O	P	3 - 174	9 - 180
1	97	THR	THR	GLN	GLN	F	G	3 - 174	9 - 180
2	97	THR	THR	GLN	GLN	P	Q	3 - 174	9 - 180
1	98	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
2	98	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	99	THR	THR	THR	THR	G	H	3 - 172	9 - 178
2	99	THR	THR	THR	THR	H	I	3 - 172	9 - 178
1	100	THR	THR	GLN	GLN	G	H	3 - 173	9 - 179
2	100	THR	THR	GLN	GLN	I	J	3 - 173	9 - 179
1	101	THR	THR	THR	THR	G	H	3 - 172	9 - 178
2	101	THR	THR	THR	THR	J	K	3 - 172	9 - 178
1	102	THR	THR	GLN	GLN	G	H	3 - 173	9 - 179
2	102	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	103	THR	THR	GLN	GLN	G	H	3 - 173	9 - 179
2	103	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	104	THR	THR	THR	THR	G	H	3 - 172	9 - 178
2	104	THR	THR	THR	THR	M	N	3 - 172	9 - 178
1	105	THR	THR	GLN	GLN	G	H	3 - 173	9 - 179
2	105	THR	THR	GLN	GLN	N	O	3 - 173	9 - 179
1	106	THR	THR	THR	THR	G	H	3 - 172	9 - 178
2	106	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	107	THR	THR	THR	THR	G	H	3 - 172	9 - 178
2	107	THR	THR	THR	THR	P	Q	3 - 172	9 - 178
1	108	THR	THR	THR	THR	G	H	3 - 172	9 - 178
2	108	THR	THR	THR	THR	Q	R	3 - 172	9 - 178
1	109	THR	THR	THR	THR	H	I	3 - 172	9 - 178
2	109	THR	THR	THR	THR	I	J	3 - 172	9 - 178
1	110	THR	THR	GLN	GLN	H	I	3 - 174	9 - 180
2	110	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
1	111	THR	THR	THR	THR	H	I	3 - 172	9 - 178
2	111	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	112	THR	THR	THR	THR	H	I	3 - 172	9 - 178
2	112	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	113	THR	THR	GLN	GLN	H	I	3 - 174	9 - 180
2	113	THR	THR	GLN	GLN	M	N	3 - 174	9 - 180
1	114	THR	THR	THR	THR	H	I	3 - 172	9 - 178
2	114	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	115	THR	THR	GLN	GLN	H	I	3 - 174	9 - 180
2	115	THR	THR	GLN	GLN	O	P	3 - 174	9 - 180
1	116	THR	THR	GLN	GLN	H	I	3 - 174	9 - 180
2	116	THR	THR	GLN	GLN	P	Q	3 - 174	9 - 180
1	117	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
2	117	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	118	THR	THR	THR	THR	I	J	3 - 172	9 - 178
2	118	THR	THR	THR	THR	J	K	3 - 172	9 - 178
1	119	THR	THR	GLN	GLN	I	J	3 - 173	9 - 179
2	119	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	120	THR	THR	GLN	GLN	I	J	3 - 173	9 - 179
2	120	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	121	THR	THR	THR	THR	I	J	3 - 172	9 - 178
2	121	THR	THR	THR	THR	M	N	3 - 172	9 - 178
1	122	THR	THR	GLN	GLN	I	J	3 - 173	9 - 179
2	122	THR	THR	GLN	GLN	N	O	3 - 173	9 - 179
1	123	THR	THR	THR	THR	I	J	3 - 172	9 - 178
2	123	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	124	THR	THR	THR	THR	I	J	3 - 172	9 - 178
2	124	THR	THR	THR	THR	P	Q	3 - 172	9 - 178
1	125	THR	THR	THR	THR	I	J	3 - 172	9 - 178
2	125	THR	THR	THR	THR	Q	R	3 - 172	9 - 178
1	126	THR	THR	THR	THR	J	K	3 - 172	9 - 178
2	126	THR	THR	THR	THR	K	L	3 - 172	9 - 178
1	127	THR	THR	THR	THR	J	K	3 - 172	9 - 178
2	127	THR	THR	THR	THR	L	M	3 - 172	9 - 178
1	128	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
2	128	THR	THR	GLN	GLN	M	N	3 - 174	9 - 180
1	129	THR	THR	THR	THR	J	K	3 - 172	9 - 178
2	129	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	130	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
2	130	THR	THR	GLN	GLN	O	P	3 - 174	9 - 180
1	131	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
2	131	THR	THR	GLN	GLN	P	Q	3 - 174	9 - 180
1	132	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
2	132	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	133	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
2	133	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	134	THR	THR	THR	THR	K	L	3 - 172	9 - 178
2	134	THR	THR	THR	THR	M	N	3 - 172	9 - 178
1	135	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
2	135	THR	THR	GLN	GLN	N	O	3 - 173	9 - 179
1	136	THR	THR	THR	THR	K	L	3 - 172	9 - 178
2	136	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	137	THR	THR	THR	THR	K	L	3 - 172	9 - 178
2	137	THR	THR	THR	THR	P	Q	3 - 172	9 - 178
1	138	THR	THR	THR	THR	K	L	3 - 172	9 - 178
2	138	THR	THR	THR	THR	Q	R	3 - 172	9 - 178
1	139	THR	THR	THR	THR	L	M	3 - 172	9 - 178
2	139	THR	THR	THR	THR	M	N	3 - 172	9 - 178
1	140	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
2	140	THR	THR	GLN	GLN	N	O	3 - 173	9 - 179
1	141	THR	THR	THR	THR	L	M	3 - 172	9 - 178
2	141	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	142	THR	THR	THR	THR	L	M	3 - 172	9 - 178
2	142	THR	THR	THR	THR	P	Q	3 - 172	9 - 178
1	143	THR	THR	THR	THR	L	M	3 - 172	9 - 178
2	143	THR	THR	THR	THR	Q	R	3 - 172	9 - 178
1	144	THR	THR	THR	THR	M	N	3 - 172	9 - 178
2	144	THR	THR	THR	THR	N	O	3 - 172	9 - 178
1	145	THR	THR	GLN	GLN	M	N	3 - 174	9 - 180
2	145	THR	THR	GLN	GLN	O	P	3 - 174	9 - 180
1	146	THR	THR	GLN	GLN	M	N	3 - 174	9 - 180
2	146	THR	THR	GLN	GLN	P	Q	3 - 174	9 - 180
1	147	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
2	147	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	148	THR	THR	THR	THR	N	O	3 - 172	9 - 178
2	148	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	149	THR	THR	THR	THR	N	O	3 - 172	9 - 178
2	149	THR	THR	THR	THR	P	Q	3 - 172	9 - 178
1	150	THR	THR	THR	THR	N	O	3 - 172	9 - 178
2	150	THR	THR	THR	THR	Q	R	3 - 172	9 - 178
1	151	THR	THR	GLN	GLN	O	P	3 - 174	9 - 180
2	151	THR	THR	GLN	GLN	P	Q	3 - 174	9 - 180
1	152	THR	THR	GLN	GLN	O	P	3 - 173	9 - 179
2	152	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	153	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
2	153	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179

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
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153

Components

#1: Protein

R A B C D E F G H I J K L M N O P Q
O-acetyl-ADP-ribose deacetylase / Regulator of RNase III activity

Details:

Mass: 19636.115 Da / Num. of mol.: 18 / Mutation: Y126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ymdB / Production host: Escherichia coli (E. coli)
References: UniProt: C3TEL7, UniProt: P0A8D6*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

#2: Chemical

R-401 A-201 B-201 C-201 D-201 E-201 F-201 G-201 H-201 I-201 J-201 K-201 L-201 M-201 N-201 O-201 P-201 Q-201
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE

Details:

Mass: 559.316 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₅O₁₄P₂

#3: Chemical

R-402 A-202 B-202 C-202 D-202 E-202 F-202 G-202 H-202 I-202 J-202 K-202 L-202 M-202 N-202 O-202 P-202 Q-202
ChemComp-SO4 / SULFATE ION / Sulfate

Details:

Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 3.93 ų/Da / Density % sol: 68.68 %
• Crystal grow: Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2 M ammonium sulfate, 0.1 M BIS-TRIS

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
• Detector: Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2015
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9791 Å / Relative weight: 1
• Reflection: Resolution: 2.98→50 Å / Num. obs: 109753 / % possible obs: 98.1 % / Redundancy: 10.6 % / R_merge(I) obs: 0.166 / Net I/σ(I): 14
• Reflection shell: Resolution: 3→3.05 Å / Redundancy: 10.9 % / R_merge(I) obs: 0.783 / Mean I/σ(I) obs: 2.8 / % possible all: 100

Processing

Software

Name	Version	Classification
REFMAC	5.7.0032	refinement
Coot		model building
HKL-2000		data processing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SPV

1spv

Resolution: 2.98→41.9 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.878 / Cross valid method: THROUGHOUT / ESU R: 1.041 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2497	5499	5 %	RANDOM
Rwork	0.2217	-	-	-
obs	0.2231	104050	97.81 %	-

• 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: 48.882 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.06 Å2	-0.06 Å2	0 Å2
2-	-	-0.06 Å2	0 Å2
3-	-	-	0.19 Å2

Refinement step

Cycle: 1 / Resolution: 2.98→41.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22679	0	720	120	23519

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	23862
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	22355
X-RAY DIFFRACTION	r_angle_refined_deg	1.841	1.986	32782
X-RAY DIFFRACTION	r_angle_other_deg	3.783	3	51073
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.043	5	3079
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.472	24.411	943
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.781	15	3308
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.284	15	121
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	3932
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	27274
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	5297
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	3.769	4.834	12370
X-RAY DIFFRACTION	r_mcbond_other	3.769	4.834	12369
X-RAY DIFFRACTION	r_mcangle_it	5.743	7.248	15431
X-RAY DIFFRACTION	r_mcangle_other	5.743	7.248	15432
X-RAY DIFFRACTION	r_scbond_it	3.999	5.179	11492
X-RAY DIFFRACTION	r_scbond_other	3.989	5.18	11421
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.071	7.643	17244
X-RAY DIFFRACTION	r_long_range_B_refined	8.383	40.249	26419
X-RAY DIFFRACTION	r_long_range_B_other	8.381	40.249	26414
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	R	9381	0.13
1	2	A	9381	0.13
2	1	R	9584	0.12
2	2	B	9584	0.12
3	1	R	9423	0.11
3	2	C	9423	0.11
4	1	R	9335	0.14
4	2	D	9335	0.14
5	1	R	9395	0.12
5	2	E	9395	0.12
6	1	R	9365	0.12
6	2	F	9365	0.12
7	1	R	9377	0.11
7	2	G	9377	0.11
8	1	R	9429	0.12
8	2	H	9429	0.12
9	1	R	9395	0.12
9	2	I	9395	0.12
10	1	R	9136	0.15
10	2	J	9136	0.15
11	1	R	9103	0.14
11	2	K	9103	0.14
12	1	R	9356	0.12
12	2	L	9356	0.12
13	1	R	9538	0.1
13	2	M	9538	0.1
14	1	R	9281	0.11
14	2	N	9281	0.11
15	1	R	9552	0.11
15	2	O	9552	0.11
16	1	R	9557	0.11
16	2	P	9557	0.11
17	1	R	9555	0.12
17	2	Q	9555	0.12
18	1	A	9636	0.14
18	2	B	9636	0.14
19	1	A	9521	0.14
19	2	C	9521	0.14
20	1	A	9391	0.15
20	2	D	9391	0.15
21	1	A	9488	0.14
21	2	E	9488	0.14
22	1	A	9205	0.13
22	2	F	9205	0.13
23	1	A	9225	0.13
23	2	G	9225	0.13
24	1	A	9143	0.14
24	2	H	9143	0.14
25	1	A	9278	0.14
25	2	I	9278	0.14
26	1	A	8999	0.16
26	2	J	8999	0.16
27	1	A	8966	0.16
27	2	K	8966	0.16
28	1	A	9163	0.14
28	2	L	9163	0.14
29	1	A	9361	0.13
29	2	M	9361	0.13
30	1	A	9064	0.14
30	2	N	9064	0.14
31	1	A	9300	0.13
31	2	O	9300	0.13
32	1	A	9381	0.14
32	2	P	9381	0.14
33	1	A	9517	0.14
33	2	Q	9517	0.14
34	1	B	10063	0.11
34	2	C	10063	0.11
35	1	B	9944	0.14
35	2	D	9944	0.14
36	1	B	9879	0.12
36	2	E	9879	0.12
37	1	B	9432	0.12
37	2	F	9432	0.12
38	1	B	9661	0.1
38	2	G	9661	0.1
39	1	B	9758	0.12
39	2	H	9758	0.12
40	1	B	9716	0.12
40	2	I	9716	0.12
41	1	B	9470	0.15
41	2	J	9470	0.15
42	1	B	9288	0.15
42	2	K	9288	0.15
43	1	B	9354	0.13
43	2	L	9354	0.13
44	1	B	9897	0.1
44	2	M	9897	0.1
45	1	B	9429	0.12
45	2	N	9429	0.12
46	1	B	9839	0.11
46	2	O	9839	0.11
47	1	B	9684	0.12
47	2	P	9684	0.12
48	1	B	9927	0.13
48	2	Q	9927	0.13
49	1	C	9822	0.14
49	2	D	9822	0.14
50	1	C	9770	0.12
50	2	E	9770	0.12
51	1	C	9422	0.12
51	2	F	9422	0.12
52	1	C	9562	0.1
52	2	G	9562	0.1
53	1	C	9604	0.11
53	2	H	9604	0.11
54	1	C	9569	0.12
54	2	I	9569	0.12
55	1	C	9425	0.15
55	2	J	9425	0.15
56	1	C	9231	0.15
56	2	K	9231	0.15
57	1	C	9319	0.13
57	2	L	9319	0.13
58	1	C	9832	0.1
58	2	M	9832	0.1
59	1	C	9342	0.11
59	2	N	9342	0.11
60	1	C	9673	0.11
60	2	O	9673	0.11
61	1	C	9688	0.11
61	2	P	9688	0.11
62	1	C	9808	0.13
62	2	Q	9808	0.13
63	1	D	9704	0.14
63	2	E	9704	0.14
64	1	D	9394	0.13
64	2	F	9394	0.13
65	1	D	9476	0.13
65	2	G	9476	0.13
66	1	D	9523	0.14
66	2	H	9523	0.14
67	1	D	9451	0.14
67	2	I	9451	0.14
68	1	D	9367	0.16
68	2	J	9367	0.16
69	1	D	9149	0.16
69	2	K	9149	0.16
70	1	D	9180	0.15
70	2	L	9180	0.15
71	1	D	9642	0.13
71	2	M	9642	0.13
72	1	D	9253	0.14
72	2	N	9253	0.14
73	1	D	9572	0.13
73	2	O	9572	0.13
74	1	D	9575	0.14
74	2	P	9575	0.14
75	1	D	9786	0.15
75	2	Q	9786	0.15
76	1	E	9423	0.12
76	2	F	9423	0.12
77	1	E	9403	0.11
77	2	G	9403	0.11
78	1	E	9414	0.12
78	2	H	9414	0.12
79	1	E	9305	0.14
79	2	I	9305	0.14
80	1	E	9261	0.16
80	2	J	9261	0.16
81	1	E	9018	0.16
81	2	K	9018	0.16
82	1	E	9261	0.13
82	2	L	9261	0.13
83	1	E	9554	0.11
83	2	M	9554	0.11
84	1	E	9140	0.13
84	2	N	9140	0.13
85	1	E	9451	0.12
85	2	O	9451	0.12
86	1	E	9621	0.12
86	2	P	9621	0.12
87	1	E	9699	0.13
87	2	Q	9699	0.13
88	1	F	9235	0.11
88	2	G	9235	0.11
89	1	F	9581	0.11
89	2	H	9581	0.11
90	1	F	9207	0.13
90	2	I	9207	0.13
91	1	F	9326	0.14
91	2	J	9326	0.14
92	1	F	9088	0.15
92	2	K	9088	0.15
93	1	F	9154	0.13
93	2	L	9154	0.13
94	1	F	9535	0.12
94	2	M	9535	0.12
95	1	F	9140	0.13
95	2	N	9140	0.13
96	1	F	9537	0.11
96	2	O	9537	0.11
97	1	F	9636	0.11
97	2	P	9636	0.11
98	1	F	9288	0.13
98	2	Q	9288	0.13
99	1	G	9536	0.09
99	2	H	9536	0.09
100	1	G	9546	0.12
100	2	I	9546	0.12
101	1	G	9155	0.15
101	2	J	9155	0.15
102	1	G	9235	0.15
102	2	K	9235	0.15
103	1	G	9378	0.12
103	2	L	9378	0.12
104	1	G	9607	0.09
104	2	M	9607	0.09
105	1	G	9381	0.1
105	2	N	9381	0.1
106	1	G	9521	0.1
106	2	O	9521	0.1
107	1	G	9406	0.11
107	2	P	9406	0.11
108	1	G	9567	0.11
108	2	Q	9567	0.11
109	1	H	9553	0.12
109	2	I	9553	0.12
110	1	H	9282	0.15
110	2	J	9282	0.15
111	1	H	9198	0.15
111	2	K	9198	0.15
112	1	H	9172	0.13
112	2	L	9172	0.13
113	1	H	9675	0.11
113	2	M	9675	0.11
114	1	H	9232	0.12
114	2	N	9232	0.12
115	1	H	9799	0.11
115	2	O	9799	0.11
116	1	H	9529	0.12
116	2	P	9529	0.12
117	1	H	9437	0.13
117	2	Q	9437	0.13
118	1	I	9188	0.16
118	2	J	9188	0.16
119	1	I	9125	0.15
119	2	K	9125	0.15
120	1	I	9287	0.14
120	2	L	9287	0.14
121	1	I	9645	0.11
121	2	M	9645	0.11
122	1	I	9328	0.13
122	2	N	9328	0.13
123	1	I	9554	0.12
123	2	O	9554	0.12
124	1	I	9462	0.13
124	2	P	9462	0.13
125	1	I	9524	0.12
125	2	Q	9524	0.12
126	1	J	9084	0.17
126	2	K	9084	0.17
127	1	J	8933	0.16
127	2	L	8933	0.16
128	1	J	9491	0.14
128	2	M	9491	0.14
129	1	J	9085	0.15
129	2	N	9085	0.15
130	1	J	9341	0.15
130	2	O	9341	0.15
131	1	J	9466	0.14
131	2	P	9466	0.14
132	1	J	9320	0.15
132	2	Q	9320	0.15
133	1	K	9055	0.16
133	2	L	9055	0.16
134	1	K	9306	0.15
134	2	M	9306	0.15
135	1	K	9102	0.16
135	2	N	9102	0.16
136	1	K	9366	0.14
136	2	O	9366	0.14
137	1	K	9194	0.15
137	2	P	9194	0.15
138	1	K	9210	0.15
138	2	Q	9210	0.15
139	1	L	9437	0.12
139	2	M	9437	0.12
140	1	L	9279	0.13
140	2	N	9279	0.13
141	1	L	9292	0.12
141	2	O	9292	0.12
142	1	L	9304	0.13
142	2	P	9304	0.13
143	1	L	9375	0.12
143	2	Q	9375	0.12
144	1	M	9460	0.11
144	2	N	9460	0.11
145	1	M	9820	0.1
145	2	O	9820	0.1
146	1	M	9747	0.11
146	2	P	9747	0.11
147	1	M	9733	0.11
147	2	Q	9733	0.11
148	1	N	9386	0.12
148	2	O	9386	0.12
149	1	N	9295	0.12
149	2	P	9295	0.12
150	1	N	9308	0.13
150	2	Q	9308	0.13
151	1	O	9666	0.12
151	2	P	9666	0.12
152	1	O	9594	0.12
152	2	Q	9594	0.12
153	1	P	9516	0.13
153	2	Q	9516	0.13

LS refinement shell

Resolution: 2.984→3.061 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.304	395	-
Rwork	0.291	7683	-
obs	-	-	98.44 %