PDB-5cb5: Structural Insights into the Mechanism of Escherichia coli Ymdb

Basic information

• Entry: Database: PDB / ID: 5cb5
• 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 / regulation of single-species biofilm formation on inanimate substrate / O-acetyl-ADP-ribose deacetylase activity / purine nucleoside binding / purine nucleoside metabolic process / endoribonuclease inhibitor 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:

ACETATE ION / ADENOSINE-5-DIPHOSPHORIBOSE / Chem-ZOD / O-acetyl-ADP-ribose deacetylase

• Biological species: Escherichia coli K12 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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	Jun 30, 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	Nov 8, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _citation.journal_id_CSD / _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

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:

• 366 kDa, 18 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	365,599	57
Polymers	353,541	18
Non-polymers	12,058	39
Water	3,855	214

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)	20,297	3
Polymers	19,641	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	8210 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)	20,297	3
Polymers	19,641	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	8100 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)	20,297	3
Polymers	19,641	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	200 Å2
ΔGint	-14 kcal/mol
Surface area	8330 Å2
Method	PISA

4

C: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,356	4
Polymers	19,641	1
Non-polymers	714	3
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	8260 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)	20,297	3
Polymers	19,641	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	8050 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)	20,297	3
Polymers	19,641	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	8260 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)	20,339	3
Polymers	19,641	1
Non-polymers	697	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

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)	20,297	3
Polymers	19,641	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	8100 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)	20,297	3
Polymers	19,641	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	180 Å2
ΔGint	-13 kcal/mol
Surface area	8160 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)	20,297	3
Polymers	19,641	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	8210 Å2
Method	PISA

11

J: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,356	4
Polymers	19,641	1
Non-polymers	714	3
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	180 Å2
ΔGint	-14 kcal/mol
Surface area	8030 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)	20,297	3
Polymers	19,641	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

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)	20,297	3
Polymers	19,641	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	7980 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)	20,339	3
Polymers	19,641	1
Non-polymers	697	2
Water	18	1

Symmetry operations:

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

Calculated values:

Buried area	180 Å2
ΔGint	-14 kcal/mol
Surface area	7810 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)	20,297	3
Polymers	19,641	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	8070 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)	20,297	3
Polymers	19,641	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	210 Å2
ΔGint	-14 kcal/mol
Surface area	8250 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)	20,297	3
Polymers	19,641	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	180 Å2
ΔGint	-13 kcal/mol
Surface area	8130 Å2
Method	PISA

18

Q: O-acetyl-ADP-ribose deacetylase

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	20,356	4
Polymers	19,641	1
Non-polymers	714	3
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	8160 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	289.140, 289.140, 114.053
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	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	1	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
1	2	LYS	LYS	THR	THR	R	A	2 - 172	8 - 178
2	2	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
1	3	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	3	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
1	4	LYS	LYS	LEU	LEU	R	A	2 - 170	8 - 176
2	4	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
1	5	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	5	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
1	6	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	6	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
1	7	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	7	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
1	8	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	8	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
1	9	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	9	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
1	10	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	10	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	11	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	11	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	12	THR	THR	GLN	GLN	R	A	3 - 173	9 - 179
2	12	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	13	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	13	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	14	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	14	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
1	15	THR	THR	THR	THR	R	A	3 - 172	9 - 178
2	15	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	16	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	16	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
1	17	LYS	LYS	GLN	GLN	R	A	2 - 174	8 - 180
2	17	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	18	LYS	LYS	THR	THR	A	B	2 - 172	8 - 178
2	18	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
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	LEU	LEU	A	B	2 - 170	8 - 176
2	20	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
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	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	22	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
1	23	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	23	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
1	24	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	24	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
1	25	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	25	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
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	GLN	GLN	A	B	3 - 173	9 - 179
2	27	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	28	THR	THR	GLN	GLN	A	B	3 - 173	9 - 179
2	28	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	29	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	29	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	30	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	30	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
1	31	THR	THR	THR	THR	A	B	3 - 172	9 - 178
2	31	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	32	LYS	LYS	GLN	GLN	A	B	2 - 174	8 - 180
2	32	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
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	THR	THR	B	C	2 - 172	8 - 178
2	34	LYS	LYS	THR	THR	C	D	2 - 172	8 - 178
1	35	LYS	LYS	LEU	LEU	B	C	2 - 170	8 - 176
2	35	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
1	36	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	36	LYS	LYS	THR	THR	E	F	2 - 172	8 - 178
1	37	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	37	LYS	LYS	THR	THR	F	G	2 - 172	8 - 178
1	38	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	38	LYS	LYS	THR	THR	G	H	2 - 172	8 - 178
1	39	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	39	LYS	LYS	THR	THR	H	I	2 - 172	8 - 178
1	40	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	40	LYS	LYS	THR	THR	I	J	2 - 172	8 - 178
1	41	THR	THR	THR	THR	B	C	3 - 172	9 - 178
2	41	THR	THR	THR	THR	J	K	3 - 172	9 - 178
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	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	44	LYS	LYS	THR	THR	M	N	2 - 172	8 - 178
1	45	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	45	LYS	LYS	THR	THR	N	O	2 - 172	8 - 178
1	46	THR	THR	THR	THR	B	C	3 - 172	9 - 178
2	46	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	47	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	47	LYS	LYS	THR	THR	P	Q	2 - 172	8 - 178
1	48	LYS	LYS	THR	THR	B	C	2 - 172	8 - 178
2	48	LYS	LYS	THR	THR	Q	R	2 - 172	8 - 178
1	49	LYS	LYS	LEU	LEU	C	D	2 - 170	8 - 176
2	49	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
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	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	51	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
1	52	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	52	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
1	53	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	53	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
1	54	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	54	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
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	GLN	GLN	C	D	3 - 173	9 - 179
2	56	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	57	THR	THR	GLN	GLN	C	D	3 - 173	9 - 179
2	57	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	58	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	58	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	59	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	59	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
1	60	THR	THR	THR	THR	C	D	3 - 172	9 - 178
2	60	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	61	LYS	LYS	GLN	GLN	C	D	2 - 174	8 - 180
2	61	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
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	LEU	LEU	D	E	2 - 170	8 - 176
2	63	LYS	LYS	LEU	LEU	E	F	2 - 170	8 - 176
1	64	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	64	LYS	LYS	LEU	LEU	F	G	2 - 170	8 - 176
1	65	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	65	LYS	LYS	LEU	LEU	G	H	2 - 170	8 - 176
1	66	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	66	LYS	LYS	LEU	LEU	H	I	2 - 170	8 - 176
1	67	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	67	LYS	LYS	LEU	LEU	I	J	2 - 170	8 - 176
1	68	THR	THR	LEU	LEU	D	E	3 - 170	9 - 176
2	68	THR	THR	LEU	LEU	J	K	3 - 170	9 - 176
1	69	THR	THR	LEU	LEU	D	E	3 - 170	9 - 176
2	69	THR	THR	LEU	LEU	K	L	3 - 170	9 - 176
1	70	THR	THR	LEU	LEU	D	E	3 - 170	9 - 176
2	70	THR	THR	LEU	LEU	L	M	3 - 170	9 - 176
1	71	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	71	LYS	LYS	LEU	LEU	M	N	2 - 170	8 - 176
1	72	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	72	LYS	LYS	LEU	LEU	N	O	2 - 170	8 - 176
1	73	THR	THR	LEU	LEU	D	E	3 - 170	9 - 176
2	73	THR	THR	LEU	LEU	O	P	3 - 170	9 - 176
1	74	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	74	LYS	LYS	LEU	LEU	P	Q	2 - 170	8 - 176
1	75	LYS	LYS	LEU	LEU	D	E	2 - 170	8 - 176
2	75	LYS	LYS	LEU	LEU	Q	R	2 - 170	8 - 176
1	76	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	76	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
1	77	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	77	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
1	78	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	78	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
1	79	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	79	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
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	GLN	GLN	E	F	3 - 173	9 - 179
2	81	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	82	THR	THR	GLN	GLN	E	F	3 - 173	9 - 179
2	82	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	83	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	83	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	84	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	84	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
1	85	THR	THR	THR	THR	E	F	3 - 172	9 - 178
2	85	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	86	LYS	LYS	GLN	GLN	E	F	2 - 174	8 - 180
2	86	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
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	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
2	88	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
1	89	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
2	89	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
1	90	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
2	90	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
1	91	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
2	91	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	92	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
2	92	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	93	THR	THR	GLN	GLN	F	G	3 - 173	9 - 179
2	93	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	94	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
2	94	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	95	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
2	95	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
1	96	THR	THR	THR	THR	F	G	3 - 172	9 - 178
2	96	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	97	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
2	97	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
1	98	LYS	LYS	GLN	GLN	F	G	2 - 174	8 - 180
2	98	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	99	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
2	99	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
1	100	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
2	100	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
1	101	THR	THR	GLN	GLN	G	H	3 - 173	9 - 179
2	101	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
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	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
2	104	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	105	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
2	105	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
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	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
2	107	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
1	108	LYS	LYS	GLN	GLN	G	H	2 - 174	8 - 180
2	108	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	109	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
2	109	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
1	110	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
2	110	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
1	111	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
2	111	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
1	112	THR	THR	GLN	GLN	H	I	3 - 173	9 - 179
2	112	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
1	113	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
2	113	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	114	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
2	114	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
1	115	THR	THR	THR	THR	H	I	3 - 172	9 - 178
2	115	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	116	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
2	116	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
1	117	LYS	LYS	GLN	GLN	H	I	2 - 174	8 - 180
2	117	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	118	THR	THR	GLN	GLN	I	J	3 - 173	9 - 179
2	118	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
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	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
2	121	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
1	122	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
2	122	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
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	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
2	124	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
1	125	LYS	LYS	GLN	GLN	I	J	2 - 174	8 - 180
2	125	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	126	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
2	126	THR	THR	GLN	GLN	K	L	3 - 174	9 - 180
1	127	THR	THR	GLN	GLN	J	K	3 - 174	9 - 180
2	127	THR	THR	GLN	GLN	L	M	3 - 174	9 - 180
1	128	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
2	128	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
1	129	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
2	129	THR	THR	GLN	GLN	N	O	3 - 173	9 - 179
1	130	THR	THR	THR	THR	J	K	3 - 172	9 - 178
2	130	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	131	THR	THR	GLN	GLN	J	K	3 - 173	9 - 179
2	131	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
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 - 174	9 - 180
2	133	THR	THR	GLN	GLN	L	M	3 - 174	9 - 180
1	134	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
2	134	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
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	GLN	GLN	K	L	3 - 173	9 - 179
2	137	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
1	138	THR	THR	GLN	GLN	K	L	3 - 173	9 - 179
2	138	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	139	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
2	139	THR	THR	GLN	GLN	M	N	3 - 173	9 - 179
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	GLN	GLN	L	M	3 - 173	9 - 179
2	142	THR	THR	GLN	GLN	P	Q	3 - 173	9 - 179
1	143	THR	THR	GLN	GLN	L	M	3 - 173	9 - 179
2	143	THR	THR	GLN	GLN	Q	R	3 - 173	9 - 179
1	144	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
2	144	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
1	145	THR	THR	THR	THR	M	N	3 - 172	9 - 178
2	145	THR	THR	THR	THR	O	P	3 - 172	9 - 178
1	146	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
2	146	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
1	147	LYS	LYS	GLN	GLN	M	N	2 - 174	8 - 180
2	147	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
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	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
2	149	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
1	150	LYS	LYS	GLN	GLN	N	O	2 - 174	8 - 180
2	150	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180
1	151	THR	THR	THR	THR	O	P	3 - 172	9 - 178
2	151	THR	THR	THR	THR	P	Q	3 - 172	9 - 178
1	152	THR	THR	THR	THR	O	P	3 - 172	9 - 178
2	152	THR	THR	THR	THR	Q	R	3 - 172	9 - 178
1	153	LYS	LYS	GLN	GLN	P	Q	2 - 174	8 - 180
2	153	LYS	LYS	GLN	GLN	Q	R	2 - 174	8 - 180

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

Protein , 1 types, 18 molecules R A B C D E F G H I J K L M N O P Q

#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: 19641.176 Da / Num. of mol.: 18 / Mutation: N25A, D35A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: ymdB / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8D6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

Non-polymers , 5 types, 253 molecules

#2: Chemical

R-201 A-201 B-201 C-201 D-201 E-201 G-201 H-201 I-201 J-201 K-201 L-201 N-201 O-201 P-201 Q-402
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE

Details:

Mass: 559.316 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₅O₁₄P₂

#3: Chemical

R-202 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-403
ChemComp-SO4 / SULFATE ION / Sulfate

Details:

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

#4: Chemical

C-203 J-203 Q-401 ChemComp-ACT / ACETATE ION / Acetate

Details:

Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂

#5: Chemical

F-201 M-201 ChemComp-ZOD / [(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate

Details:

Mass: 601.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₅N₅O₁₅P₂

#6: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 3.89 ų/Da / Density % sol: 68.4 %
• 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: BL17U / Wavelength: 0.9791 Å
• Detector: Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 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: 2.8→50 Å / Num. obs: 133057 / % possible obs: 98.9 % / Redundancy: 3.6 % / R_merge(I) obs: 0.114 / Net I/σ(I): 12.7
• Reflection shell: Resolution: 2.8→2.85 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.386 / Mean I/σ(I) obs: 3.1 / % possible all: 98.9

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: 2.8→38.72 Å / Cor.coef. F_o:F_c: 0.857 / Cor.coef. F_o:F_c free: 0.813 / Cross valid method: THROUGHOUT / ESU R: 0.659 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.29036	6667	5 %	RANDOM
Rwork	0.26153	-	-	-
obs	0.26296	126269	98.85 %	-

• 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: 38.947 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.04 Å2	0.04 Å2	-0 Å2
2-	-	0.04 Å2	-0 Å2
3-	-	-	-0.14 Å2

Refinement step

Cycle: 1 / Resolution: 2.8→38.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22926	0	756	214	23896

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	24162
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	22764
X-RAY DIFFRACTION	r_angle_refined_deg	1.896	1.989	33153
X-RAY DIFFRACTION	r_angle_other_deg	3.865	3	52044
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.385	5	3087
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.852	23.996	951
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.363	15	3414
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.846	15	134
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	3946
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	27415
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	5379
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	2.672	3.871	12405
X-RAY DIFFRACTION	r_mcbond_other	2.671	3.871	12404
X-RAY DIFFRACTION	r_mcangle_it	4.274	5.798	15471
X-RAY DIFFRACTION	r_mcangle_other	4.274	5.799	15472
X-RAY DIFFRACTION	r_scbond_it	2.535	4.053	11756
X-RAY DIFFRACTION	r_scbond_other	2.535	4.053	11753
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.047	5.968	17677
X-RAY DIFFRACTION	r_long_range_B_refined	6.804	31.499	26271
X-RAY DIFFRACTION	r_long_range_B_other	6.804	31.5	26271
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	9303	0.13
1	2	A	9303	0.13
2	1	R	9704	0.12
2	2	B	9704	0.12
3	1	R	9695	0.12
3	2	C	9695	0.12
4	1	R	8953	0.14
4	2	D	8953	0.14
5	1	R	9824	0.11
5	2	E	9824	0.11
6	1	R	9453	0.14
6	2	F	9453	0.14
7	1	R	9697	0.11
7	2	G	9697	0.11
8	1	R	9627	0.12
8	2	H	9627	0.12
9	1	R	9655	0.12
9	2	I	9655	0.12
10	1	R	9371	0.13
10	2	J	9371	0.13
11	1	R	9268	0.12
11	2	K	9268	0.12
12	1	R	9665	0.11
12	2	L	9665	0.11
13	1	R	9667	0.11
13	2	M	9667	0.11
14	1	R	9269	0.13
14	2	N	9269	0.13
15	1	R	9443	0.12
15	2	O	9443	0.12
16	1	R	9741	0.11
16	2	P	9741	0.11
17	1	R	9709	0.12
17	2	Q	9709	0.12
18	1	A	9198	0.13
18	2	B	9198	0.13
19	1	A	9280	0.14
19	2	C	9280	0.14
20	1	A	8756	0.13
20	2	D	8756	0.13
21	1	A	9439	0.12
21	2	E	9439	0.12
22	1	A	9077	0.15
22	2	F	9077	0.15
23	1	A	9205	0.14
23	2	G	9205	0.14
24	1	A	9253	0.14
24	2	H	9253	0.14
25	1	A	9268	0.13
25	2	I	9268	0.13
26	1	A	9024	0.14
26	2	J	9024	0.14
27	1	A	9006	0.13
27	2	K	9006	0.13
28	1	A	9101	0.12
28	2	L	9101	0.12
29	1	A	9269	0.13
29	2	M	9269	0.13
30	1	A	9080	0.14
30	2	N	9080	0.14
31	1	A	9042	0.13
31	2	O	9042	0.13
32	1	A	9316	0.12
32	2	P	9316	0.12
33	1	A	9299	0.13
33	2	Q	9299	0.13
34	1	B	9835	0.11
34	2	C	9835	0.11
35	1	B	9136	0.13
35	2	D	9136	0.13
36	1	B	9768	0.12
36	2	E	9768	0.12
37	1	B	9365	0.15
37	2	F	9365	0.15
38	1	B	9729	0.11
38	2	G	9729	0.11
39	1	B	9714	0.12
39	2	H	9714	0.12
40	1	B	9724	0.12
40	2	I	9724	0.12
41	1	B	9529	0.13
41	2	J	9529	0.13
42	1	B	9285	0.12
42	2	K	9285	0.12
43	1	B	9442	0.12
43	2	L	9442	0.12
44	1	B	9748	0.11
44	2	M	9748	0.11
45	1	B	9347	0.13
45	2	N	9347	0.13
46	1	B	9556	0.12
46	2	O	9556	0.12
47	1	B	9664	0.11
47	2	P	9664	0.11
48	1	B	9813	0.11
48	2	Q	9813	0.11
49	1	C	9089	0.13
49	2	D	9089	0.13
50	1	C	9820	0.11
50	2	E	9820	0.11
51	1	C	9447	0.14
51	2	F	9447	0.14
52	1	C	9688	0.11
52	2	G	9688	0.11
53	1	C	9757	0.13
53	2	H	9757	0.13
54	1	C	9730	0.12
54	2	I	9730	0.12
55	1	C	9521	0.12
55	2	J	9521	0.12
56	1	C	9336	0.12
56	2	K	9336	0.12
57	1	C	9438	0.11
57	2	L	9438	0.11
58	1	C	9862	0.11
58	2	M	9862	0.11
59	1	C	9356	0.12
59	2	N	9356	0.12
60	1	C	9602	0.11
60	2	O	9602	0.11
61	1	C	9793	0.11
61	2	P	9793	0.11
62	1	C	9837	0.11
62	2	Q	9837	0.11
63	1	D	9107	0.12
63	2	E	9107	0.12
64	1	D	8769	0.15
64	2	F	8769	0.15
65	1	D	8956	0.13
65	2	G	8956	0.13
66	1	D	9030	0.13
66	2	H	9030	0.13
67	1	D	9058	0.12
67	2	I	9058	0.12
68	1	D	8890	0.14
68	2	J	8890	0.14
69	1	D	8856	0.13
69	2	K	8856	0.13
70	1	D	8894	0.13
70	2	L	8894	0.13
71	1	D	9058	0.13
71	2	M	9058	0.13
72	1	D	8923	0.13
72	2	N	8923	0.13
73	1	D	8969	0.14
73	2	O	8969	0.14
74	1	D	9024	0.12
74	2	P	9024	0.12
75	1	D	9135	0.12
75	2	Q	9135	0.12
76	1	E	9518	0.15
76	2	F	9518	0.15
77	1	E	9732	0.11
77	2	G	9732	0.11
78	1	E	9742	0.12
78	2	H	9742	0.12
79	1	E	9633	0.12
79	2	I	9633	0.12
80	1	E	9416	0.12
80	2	J	9416	0.12
81	1	E	9302	0.12
81	2	K	9302	0.12
82	1	E	9599	0.11
82	2	L	9599	0.11
83	1	E	9690	0.12
83	2	M	9690	0.12
84	1	E	9430	0.13
84	2	N	9430	0.13
85	1	E	9443	0.12
85	2	O	9443	0.12
86	1	E	9814	0.11
86	2	P	9814	0.11
87	1	E	9868	0.11
87	2	Q	9868	0.11
88	1	F	9315	0.15
88	2	G	9315	0.15
89	1	F	9675	0.14
89	2	H	9675	0.14
90	1	F	9362	0.14
90	2	I	9362	0.14
91	1	F	9168	0.14
91	2	J	9168	0.14
92	1	F	9156	0.14
92	2	K	9156	0.14
93	1	F	9320	0.14
93	2	L	9320	0.14
94	1	F	9541	0.14
94	2	M	9541	0.14
95	1	F	9128	0.14
95	2	N	9128	0.14
96	1	F	9403	0.13
96	2	O	9403	0.13
97	1	F	9593	0.13
97	2	P	9593	0.13
98	1	F	9403	0.15
98	2	Q	9403	0.15
99	1	G	9787	0.11
99	2	H	9787	0.11
100	1	G	9676	0.12
100	2	I	9676	0.12
101	1	G	9474	0.12
101	2	J	9474	0.12
102	1	G	9266	0.12
102	2	K	9266	0.12
103	1	G	9490	0.12
103	2	L	9490	0.12
104	1	G	9627	0.11
104	2	M	9627	0.11
105	1	G	9390	0.12
105	2	N	9390	0.12
106	1	G	9473	0.12
106	2	O	9473	0.12
107	1	G	9628	0.11
107	2	P	9628	0.11
108	1	G	9808	0.11
108	2	Q	9808	0.11
109	1	H	9765	0.12
109	2	I	9765	0.12
110	1	H	9497	0.13
110	2	J	9497	0.13
111	1	H	9526	0.12
111	2	K	9526	0.12
112	1	H	9415	0.12
112	2	L	9415	0.12
113	1	H	9811	0.12
113	2	M	9811	0.12
114	1	H	9411	0.13
114	2	N	9411	0.13
115	1	H	9631	0.13
115	2	O	9631	0.13
116	1	H	9679	0.12
116	2	P	9679	0.12
117	1	H	9727	0.12
117	2	Q	9727	0.12
118	1	I	9439	0.13
118	2	J	9439	0.13
119	1	I	9344	0.12
119	2	K	9344	0.12
120	1	I	9457	0.11
120	2	L	9457	0.11
121	1	I	9733	0.11
121	2	M	9733	0.11
122	1	I	9357	0.12
122	2	N	9357	0.12
123	1	I	9584	0.12
123	2	O	9584	0.12
124	1	I	9726	0.11
124	2	P	9726	0.11
125	1	I	9797	0.11
125	2	Q	9797	0.11
126	1	J	9374	0.13
126	2	K	9374	0.13
127	1	J	9330	0.14
127	2	L	9330	0.14
128	1	J	9517	0.12
128	2	M	9517	0.12
129	1	J	9132	0.12
129	2	N	9132	0.12
130	1	J	9399	0.13
130	2	O	9399	0.13
131	1	J	9445	0.11
131	2	P	9445	0.11
132	1	J	9555	0.12
132	2	Q	9555	0.12
133	1	K	9243	0.12
133	2	L	9243	0.12
134	1	K	9369	0.11
134	2	M	9369	0.11
135	1	K	9167	0.12
135	2	N	9167	0.12
136	1	K	9403	0.12
136	2	O	9403	0.12
137	1	K	9173	0.12
137	2	P	9173	0.12
138	1	K	9401	0.12
138	2	Q	9401	0.12
139	1	L	9440	0.11
139	2	M	9440	0.11
140	1	L	9081	0.12
140	2	N	9081	0.12
141	1	L	9408	0.11
141	2	O	9408	0.11
142	1	L	9590	0.11
142	2	P	9590	0.11
143	1	L	9483	0.12
143	2	Q	9483	0.12
144	1	M	9455	0.11
144	2	N	9455	0.11
145	1	M	9572	0.11
145	2	O	9572	0.11
146	1	M	9696	0.11
146	2	P	9696	0.11
147	1	M	9737	0.12
147	2	Q	9737	0.12
148	1	N	9158	0.12
148	2	O	9158	0.12
149	1	N	9340	0.11
149	2	P	9340	0.11
150	1	N	9419	0.13
150	2	Q	9419	0.13
151	1	O	9511	0.1
151	2	P	9511	0.1
152	1	O	9576	0.12
152	2	Q	9576	0.12
153	1	P	9762	0.11
153	2	Q	9762	0.11

LS refinement shell

Resolution: 2.798→2.87 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.345	445	-
Rwork	0.332	9256	-
obs	-	-	98.73 %