PDB-4mvj: 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3-ph...

Basic information

• Entry: Database: PDB / ID: 4mvj
• Title: 2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3-phosphate Dehydrogenase A (gapA) from Escherichia coli Modified by Acetyl Phosphate.
• Components: (Glyceraldehyde-3-phosphate Dehydrogenase ...) x 9
• Keywords: OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / N-terminal NAD binding domain

Function / homology

Domain/homology:

Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / PYROPHOSPHATE 2- / ACETYLPHOSPHATE / :

• Biological species: Escherichia coli (E. coli)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
• Authors: Minasov, G. / Kuhn, M. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
• Citation: Journal: Plos One / Year: 2014; Title: Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation.; Authors: Kuhn, M.L. / Zemaitaitis, B. / Hu, L.I. / Sahu, A. / Sorensen, D. / Minasov, G. / Lima, B.P. / Scholle, M. / Mrksich, M. / Anderson, W.F. / Gibson, B.W. / Schilling, B. / Wolfe, A.J.

History

Deposition	Sep 24, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2014	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Assembly

Deposited unit

A: Glyceraldehyde-3-phosphate dehydrogenase A

B: Glyceraldehyde-3-phosphate dehydrogenase A

C: Glyceraldehyde-3-phosphate dehydrogenase A

D: Glyceraldehyde-3-phosphate dehydrogenase A

E: Glyceraldehyde-3-phosphate Dehydrogenase A

F: Glyceraldehyde-3-phosphate Dehydrogenase A

G: Glyceraldehyde-3-phosphate Dehydrogenase A

H: Glyceraldehyde-3-phosphate Dehydrogenase A

I: Glyceraldehyde-3-phosphate Dehydrogenase A

J: Glyceraldehyde-3-phosphate Dehydrogenase A

K: Glyceraldehyde-3-phosphate dehydrogenase A

L: Glyceraldehyde-3-phosphate dehydrogenase A

M: Glyceraldehyde-3-phosphate Dehydrogenase A

N: Glyceraldehyde-3-phosphate dehydrogenase A

O: Glyceraldehyde-3-phosphate Dehydrogenase A

P: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

• 624 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	623,957	110
Polymers	614,170	16
Non-polymers	9,787	94
Water	7,981	443

1

A: Glyceraldehyde-3-phosphate dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,988	10
Polymers	38,362	1
Non-polymers	626	9
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

2

B: Glyceraldehyde-3-phosphate dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,892	11
Polymers	38,362	1
Non-polymers	530	10
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

3

C: Glyceraldehyde-3-phosphate dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,226	8
Polymers	38,362	1
Non-polymers	864	7
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

4

D: Glyceraldehyde-3-phosphate dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,375	10
Polymers	38,321	1
Non-polymers	1,054	9
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

5

E: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,362	9
Polymers	38,403	1
Non-polymers	959	8
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

6

F: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,710	4
Polymers	38,403	1
Non-polymers	306	3
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

7

G: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,745	7
Polymers	38,404	1
Non-polymers	341	6
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

8

H: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,914	7
Polymers	38,445	1
Non-polymers	469	6
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

9

I: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,297	6
Polymers	38,444	1
Non-polymers	852	5
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

10

J: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,034	7
Polymers	38,403	1
Non-polymers	631	6
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

11

K: Glyceraldehyde-3-phosphate dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,262	9
Polymers	38,362	1
Non-polymers	899	8
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

12

L: Glyceraldehyde-3-phosphate dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,452	3
Polymers	38,321	1
Non-polymers	130	2
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

13

M: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,772	6
Polymers	38,362	1
Non-polymers	410	5
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

14

N: Glyceraldehyde-3-phosphate dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,421	3
Polymers	38,362	1
Non-polymers	58	2
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

15

O: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,138	4
Polymers	38,403	1
Non-polymers	734	3
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

16

P: Glyceraldehyde-3-phosphate Dehydrogenase A

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	39,370	6
Polymers	38,445	1
Non-polymers	924	5
Water	18	1

Symmetry operations:

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

Calculated values:

Method	PISA

Unit cell

Length a, b, c (Å)	145.879, 69.688, 271.923
Angle α, β, γ (deg.)	90.00, 98.80, 90.00
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	SER	SER	A	A	1 - 330	25 - 354
2	1	MET	MET	SER	SER	B	B	1 - 330	25 - 354
1	2	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	2	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
1	3	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	3	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
1	4	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	4	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
1	5	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	5	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
1	6	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	6	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
1	7	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	7	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
1	8	THR	THR	SER	SER	A	A	2 - 330	26 - 354
2	8	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	9	THR	THR	SER	SER	A	A	2 - 330	26 - 354
2	9	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	10	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	10	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
1	11	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	11	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	12	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	12	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	13	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	13	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	14	MET	MET	LYS	LYS	A	A	1 - 331	25 - 355
2	14	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	15	THR	THR	SER	SER	A	A	2 - 330	26 - 354
2	15	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	16	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	16	MET	MET	SER	SER	C	C	1 - 330	25 - 354
1	17	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	17	MET	MET	SER	SER	D	D	1 - 330	25 - 354
1	18	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	18	MET	MET	SER	SER	E	E	1 - 330	25 - 354
1	19	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	19	MET	MET	SER	SER	F	F	1 - 330	25 - 354
1	20	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	20	MET	MET	SER	SER	G	G	1 - 330	25 - 354
1	21	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	21	MET	MET	SER	SER	H	H	1 - 330	25 - 354
1	22	THR	THR	SER	SER	B	B	2 - 330	26 - 354
2	22	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	23	THR	THR	SER	SER	B	B	2 - 330	26 - 354
2	23	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	24	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	24	MET	MET	SER	SER	K	K	1 - 330	25 - 354
1	25	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	25	MET	MET	SER	SER	L	L	1 - 330	25 - 354
1	26	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	26	MET	MET	SER	SER	M	M	1 - 330	25 - 354
1	27	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	27	MET	MET	SER	SER	N	N	1 - 330	25 - 354
1	28	MET	MET	SER	SER	B	B	1 - 330	25 - 354
2	28	MET	MET	SER	SER	O	O	1 - 330	25 - 354
1	29	THR	THR	SER	SER	B	B	2 - 330	26 - 354
2	29	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	30	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	30	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
1	31	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	31	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
1	32	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	32	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
1	33	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	33	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
1	34	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	34	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
1	35	THR	THR	SER	SER	C	C	2 - 330	26 - 354
2	35	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	36	THR	THR	SER	SER	C	C	2 - 330	26 - 354
2	36	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	37	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	37	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
1	38	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	38	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	39	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	39	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	40	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	40	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	41	MET	MET	LYS	LYS	C	C	1 - 331	25 - 355
2	41	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	42	THR	THR	SER	SER	C	C	2 - 330	26 - 354
2	42	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	43	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	43	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
1	44	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	44	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
1	45	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	45	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
1	46	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	46	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
1	47	THR	THR	SER	SER	D	D	2 - 330	26 - 354
2	47	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	48	THR	THR	SER	SER	D	D	2 - 330	26 - 354
2	48	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	49	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	49	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
1	50	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	50	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	51	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	51	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	52	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	52	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	53	MET	MET	LYS	LYS	D	D	1 - 331	25 - 355
2	53	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	54	THR	THR	SER	SER	D	D	2 - 330	26 - 354
2	54	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	55	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	55	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
1	56	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	56	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
1	57	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	57	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
1	58	THR	THR	SER	SER	E	E	2 - 330	26 - 354
2	58	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	59	THR	THR	SER	SER	E	E	2 - 330	26 - 354
2	59	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	60	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	60	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
1	61	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	61	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	62	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	62	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	63	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	63	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	64	MET	MET	LYS	LYS	E	E	1 - 331	25 - 355
2	64	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	65	THR	THR	SER	SER	E	E	2 - 330	26 - 354
2	65	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	66	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
2	66	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
1	67	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
2	67	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
1	68	THR	THR	SER	SER	F	F	2 - 330	26 - 354
2	68	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	69	THR	THR	SER	SER	F	F	2 - 330	26 - 354
2	69	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	70	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
2	70	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
1	71	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
2	71	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	72	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
2	72	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	73	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
2	73	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	74	MET	MET	LYS	LYS	F	F	1 - 331	25 - 355
2	74	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	75	THR	THR	SER	SER	F	F	2 - 330	26 - 354
2	75	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	76	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
2	76	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
1	77	THR	THR	SER	SER	G	G	2 - 330	26 - 354
2	77	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	78	THR	THR	SER	SER	G	G	2 - 330	26 - 354
2	78	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	79	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
2	79	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
1	80	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
2	80	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	81	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
2	81	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	82	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
2	82	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	83	MET	MET	LYS	LYS	G	G	1 - 331	25 - 355
2	83	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	84	THR	THR	SER	SER	G	G	2 - 330	26 - 354
2	84	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	85	THR	THR	SER	SER	H	H	2 - 330	26 - 354
2	85	THR	THR	SER	SER	I	I	2 - 330	26 - 354
1	86	THR	THR	SER	SER	H	H	2 - 330	26 - 354
2	86	THR	THR	SER	SER	J	J	2 - 330	26 - 354
1	87	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
2	87	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
1	88	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
2	88	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	89	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
2	89	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	90	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
2	90	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	91	MET	MET	LYS	LYS	H	H	1 - 331	25 - 355
2	91	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	92	THR	THR	SER	SER	H	H	2 - 330	26 - 354
2	92	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	93	THR	THR	LYS	LYS	I	I	2 - 331	26 - 355
2	93	THR	THR	LYS	LYS	J	J	2 - 331	26 - 355
1	94	THR	THR	SER	SER	I	I	2 - 330	26 - 354
2	94	THR	THR	SER	SER	K	K	2 - 330	26 - 354
1	95	THR	THR	SER	SER	I	I	2 - 330	26 - 354
2	95	THR	THR	SER	SER	L	L	2 - 330	26 - 354
1	96	THR	THR	SER	SER	I	I	2 - 330	26 - 354
2	96	THR	THR	SER	SER	M	M	2 - 330	26 - 354
1	97	THR	THR	SER	SER	I	I	2 - 330	26 - 354
2	97	THR	THR	SER	SER	N	N	2 - 330	26 - 354
1	98	THR	THR	SER	SER	I	I	2 - 330	26 - 354
2	98	THR	THR	SER	SER	O	O	2 - 330	26 - 354
1	99	THR	THR	LYS	LYS	I	I	2 - 331	26 - 355
2	99	THR	THR	LYS	LYS	P	P	2 - 331	26 - 355
1	100	THR	THR	SER	SER	J	J	2 - 330	26 - 354
2	100	THR	THR	SER	SER	K	K	2 - 330	26 - 354
1	101	THR	THR	SER	SER	J	J	2 - 330	26 - 354
2	101	THR	THR	SER	SER	L	L	2 - 330	26 - 354
1	102	THR	THR	SER	SER	J	J	2 - 330	26 - 354
2	102	THR	THR	SER	SER	M	M	2 - 330	26 - 354
1	103	THR	THR	SER	SER	J	J	2 - 330	26 - 354
2	103	THR	THR	SER	SER	N	N	2 - 330	26 - 354
1	104	THR	THR	SER	SER	J	J	2 - 330	26 - 354
2	104	THR	THR	SER	SER	O	O	2 - 330	26 - 354
1	105	THR	THR	LYS	LYS	J	J	2 - 331	26 - 355
2	105	THR	THR	LYS	LYS	P	P	2 - 331	26 - 355
1	106	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
2	106	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
1	107	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
2	107	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	108	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
2	108	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	109	MET	MET	LYS	LYS	K	K	1 - 331	25 - 355
2	109	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	110	THR	THR	SER	SER	K	K	2 - 330	26 - 354
2	110	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	111	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
2	111	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
1	112	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
2	112	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	113	MET	MET	LYS	LYS	L	L	1 - 331	25 - 355
2	113	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	114	THR	THR	SER	SER	L	L	2 - 330	26 - 354
2	114	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	115	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
2	115	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
1	116	MET	MET	LYS	LYS	M	M	1 - 331	25 - 355
2	116	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	117	THR	THR	SER	SER	M	M	2 - 330	26 - 354
2	117	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	118	MET	MET	LYS	LYS	N	N	1 - 331	25 - 355
2	118	MET	MET	LYS	LYS	O	O	1 - 331	25 - 355
1	119	THR	THR	SER	SER	N	N	2 - 330	26 - 354
2	119	THR	THR	SER	SER	P	P	2 - 330	26 - 354
1	120	THR	THR	SER	SER	O	O	2 - 330	26 - 354
2	120	THR	THR	SER	SER	P	P	2 - 330	26 - 354

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

Components

Glyceraldehyde-3-phosphate Dehydrogenase ... , 9 types, 16 molecules A B C K N D L E F J O G H I M P

#1: Protein

A B C K N
Glyceraldehyde-3-phosphate dehydrogenase A / Glyceraldehyde-3-phosphate dehydrogenase / type I

Details:

Mass: 38362.375 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#2: Protein

D L Glyceraldehyde-3-phosphate dehydrogenase A / Glyceraldehyde-3-phosphate dehydrogenase / type I

Details:

Mass: 38321.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#3: Protein

E Glyceraldehyde-3-phosphate Dehydrogenase A

Details:

Mass: 38403.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#4: Protein

F J O Glyceraldehyde-3-phosphate Dehydrogenase A

Details:

Mass: 38403.402 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#5: Protein

G Glyceraldehyde-3-phosphate Dehydrogenase A

Details:

Mass: 38404.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#6: Protein

H Glyceraldehyde-3-phosphate Dehydrogenase A

Details:

Mass: 38445.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#7: Protein

I Glyceraldehyde-3-phosphate Dehydrogenase A

Details:

Mass: 38444.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#8: Protein

M Glyceraldehyde-3-phosphate Dehydrogenase A

Details:

Mass: 38362.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

#9: Protein

P Glyceraldehyde-3-phosphate Dehydrogenase A

Details:

Mass: 38445.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655, DH1 / Gene: ECDH1ME8569_1723, EcDH1_1863, gapA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: C9QTS9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

Non-polymers , 11 types, 537 molecules

#10: Chemical

A-401 B-401 B-402 C-402 D-402 E-402 G-401 H-401 I-402 K-402 M-401 N-401
ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na

#11: Chemical

A-402 A-403 A-404 A-405 B-403 B-404 B-405 B-406 B-407 B-408 C-403 C-404 C-405 C-406 C-407 D-403 D-404 D-405 D-406 D-407 ...
ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 49 / Source method: obtained synthetically / Formula: Cl

#12: Chemical

A-406 A-407 A-408 B-409 D-408 D-409 E-408 F-402 H-403 I-405 J-403 J-404 L-402 P-404 P-405
ChemComp-PO4 / PHOSPHATE ION

Details:

Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO₄

#13: Chemical

A-409 B-410 F-403 G-406 J-406 M-405
ChemComp-POP / PYROPHOSPHATE 2-

Details:

Mass: 175.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H₂O₇P₂

#14: Chemical

C-401 D-401 E-401 I-401 K-401 O-401 P-401
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Details:

Mass: 663.425 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM

#15: Chemical

H-404 ChemComp-ACT / ACETATE ION

Details:

Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂

#16: Chemical

H-405 ChemComp-PGE / TRIETHYLENE GLYCOL

Details:

Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄

#17: Chemical

H-406 ChemComp-PEG / DI(HYDROXYETHYL)ETHER

Details:

Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃

#18: Chemical

J-405 ChemComp-PG4 / TETRAETHYLENE GLYCOL

Details:

Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM

#19: Chemical

M-404 ChemComp-UVW / ACETYLPHOSPHATE

Details:

Mass: 140.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₅O₅P

#20: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 2.22 ų/Da / Density % sol: 44.69 %
• Crystal grow: Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 ; Details: Protein - 7.3mg/mL, 0.15M Sodium chloride, 0.01M Tris-HCl pH 8.3, Screen - PACT (G2), 0.2 M Sodium bromide, 0.1 M Bis Tris propane pH 7.5, 20 % (w/v) PEG 3350, 10mM ACP., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
• Detector: Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2013 / Details: Beryllium lenses
• Radiation: Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97872 Å / Relative weight: 1
• Reflection: Resolution: 2.85→30 Å / Num. all: 127301 / Num. obs: 127301 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 75.3 Ų / R_merge(I) obs: 0.086 / Net I/σ(I): 15.5
• Reflection shell: Resolution: 2.85→2.9 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.637 / Mean I/σ(I) obs: 2 / Num. unique all: 6384 / % possible all: 100

Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHASER		phasing
REFMAC	5.8.0046	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7C

1s7c

Resolution: 2.85→29.91 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.918 / SU B: 34.605 / SU ML: 0.317
Isotropic thermal model: Thermal Factors Isotropically Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2235	6389	5 %	RANDOM
Rwork	0.18582	-	-	-
all	0.18774	120750	-	-
obs	0.18774	120750	99.8 %	-

• 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: 74.416 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-1.56 Å2	0 Å2	-1.03 Å2
2-	-	1.44 Å2	0 Å2
3-	-	-	0.42 Å2

Refinement step

Cycle: LAST / Resolution: 2.85→29.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	39992	0	540	443	40975

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	41307
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	39806
X-RAY DIFFRACTION	r_angle_refined_deg	1.904	1.968	56037
X-RAY DIFFRACTION	r_angle_other_deg	1.315	3	91589
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.17	5	5316
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.67	24.931	1667
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.892	15	6932
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.904	15	193
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	6505
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	46868
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	8869
X-RAY DIFFRACTION	r_mcbond_it	3.92	3.523	21256
X-RAY DIFFRACTION	r_mcbond_other	3.919	3.522	21254
X-RAY DIFFRACTION	r_mcangle_it	5.884	5.285	26574
X-RAY DIFFRACTION	r_mcangle_other	5.884	5.286	26575
X-RAY DIFFRACTION	r_scbond_it	5.412	3.981	20051
X-RAY DIFFRACTION	r_scbond_other	5.365	3.977	20003
X-RAY DIFFRACTION	r_scangle_other	7.667	5.762	29386
X-RAY DIFFRACTION	r_long_range_B_refined	9.968	28.266	45074
X-RAY DIFFRACTION	r_long_range_B_other	9.952	28.25	45029

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	20278	0.06
1	2	B	20278	0.06
2	1	A	20418	0.06
2	2	C	20418	0.06
3	1	A	20355	0.06
3	2	D	20355	0.06
4	1	A	20436	0.05
4	2	E	20436	0.05
5	1	A	20397	0.05
5	2	F	20397	0.05
6	1	A	20504	0.04
6	2	G	20504	0.04
7	1	A	20385	0.05
7	2	H	20385	0.05
8	1	A	20209	0.05
8	2	I	20209	0.05
9	1	A	20277	0.05
9	2	J	20277	0.05
10	1	A	20481	0.05
10	2	K	20481	0.05
11	1	A	20374	0.05
11	2	L	20374	0.05
12	1	A	20256	0.06
12	2	M	20256	0.06
13	1	A	20506	0.05
13	2	N	20506	0.05
14	1	A	20425	0.05
14	2	O	20425	0.05
15	1	A	20358	0.04
15	2	P	20358	0.04
16	1	B	20164	0.07
16	2	C	20164	0.07
17	1	B	20178	0.06
17	2	D	20178	0.06
18	1	B	20146	0.06
18	2	E	20146	0.06
19	1	B	20134	0.06
19	2	F	20134	0.06
20	1	B	20259	0.06
20	2	G	20259	0.06
21	1	B	20151	0.06
21	2	H	20151	0.06
22	1	B	20100	0.06
22	2	I	20100	0.06
23	1	B	20134	0.06
23	2	J	20134	0.06
24	1	B	20260	0.06
24	2	K	20260	0.06
25	1	B	20155	0.06
25	2	L	20155	0.06
26	1	B	20088	0.06
26	2	M	20088	0.06
27	1	B	20258	0.06
27	2	N	20258	0.06
28	1	B	20177	0.06
28	2	O	20177	0.06
29	1	B	20201	0.05
29	2	P	20201	0.05
30	1	C	20263	0.06
30	2	D	20263	0.06
31	1	C	20398	0.05
31	2	E	20398	0.05
32	1	C	20374	0.05
32	2	F	20374	0.05
33	1	C	20487	0.04
33	2	G	20487	0.04
34	1	C	20371	0.04
34	2	H	20371	0.04
35	1	C	20222	0.05
35	2	I	20222	0.05
36	1	C	20290	0.04
36	2	J	20290	0.04
37	1	C	20464	0.04
37	2	K	20464	0.04
38	1	C	20356	0.05
38	2	L	20356	0.05
39	1	C	20200	0.06
39	2	M	20200	0.06
40	1	C	20470	0.04
40	2	N	20470	0.04
41	1	C	20452	0.04
41	2	O	20452	0.04
42	1	C	20277	0.04
42	2	P	20277	0.04
43	1	D	20202	0.06
43	2	E	20202	0.06
44	1	D	20211	0.06
44	2	F	20211	0.06
45	1	D	20321	0.05
45	2	G	20321	0.05
46	1	D	20178	0.06
46	2	H	20178	0.06
47	1	D	20060	0.06
47	2	I	20060	0.06
48	1	D	20124	0.05
48	2	J	20124	0.05
49	1	D	20313	0.05
49	2	K	20313	0.05
50	1	D	20327	0.06
50	2	L	20327	0.06
51	1	D	20279	0.06
51	2	M	20279	0.06
52	1	D	20313	0.06
52	2	N	20313	0.06
53	1	D	20259	0.05
53	2	O	20259	0.05
54	1	D	20170	0.05
54	2	P	20170	0.05
55	1	E	20368	0.04
55	2	F	20368	0.04
56	1	E	20466	0.04
56	2	G	20466	0.04
57	1	E	20345	0.04
57	2	H	20345	0.04
58	1	E	20291	0.04
58	2	I	20291	0.04
59	1	E	20264	0.04
59	2	J	20264	0.04
60	1	E	20453	0.04
60	2	K	20453	0.04
61	1	E	20368	0.04
61	2	L	20368	0.04
62	1	E	20180	0.05
62	2	M	20180	0.05
63	1	E	20473	0.04
63	2	N	20473	0.04
64	1	E	20402	0.04
64	2	O	20402	0.04
65	1	E	20390	0.04
65	2	P	20390	0.04
66	1	F	20444	0.03
66	2	G	20444	0.03
67	1	F	20498	0.04
67	2	H	20498	0.04
68	1	F	20262	0.04
68	2	I	20262	0.04
69	1	F	20336	0.04
69	2	J	20336	0.04
70	1	F	20434	0.04
70	2	K	20434	0.04
71	1	F	20318	0.04
71	2	L	20318	0.04
72	1	F	20256	0.06
72	2	M	20256	0.06
73	1	F	20449	0.03
73	2	N	20449	0.03
74	1	F	20484	0.04
74	2	O	20484	0.04
75	1	F	20233	0.04
75	2	P	20233	0.04
76	1	G	20471	0.03
76	2	H	20471	0.03
77	1	G	20248	0.03
77	2	I	20248	0.03
78	1	G	20334	0.02
78	2	J	20334	0.02
79	1	G	20548	0.03
79	2	K	20548	0.03
80	1	G	20437	0.03
80	2	L	20437	0.03
81	1	G	20270	0.05
81	2	M	20270	0.05
82	1	G	20570	0.02
82	2	N	20570	0.02
83	1	G	20474	0.02
83	2	O	20474	0.02
84	1	G	20385	0.03
84	2	P	20385	0.03
85	1	H	20269	0.04
85	2	I	20269	0.04
86	1	H	20309	0.04
86	2	J	20309	0.04
87	1	H	20431	0.03
87	2	K	20431	0.03
88	1	H	20324	0.03
88	2	L	20324	0.03
89	1	H	20255	0.05
89	2	M	20255	0.05
90	1	H	20423	0.03
90	2	N	20423	0.03
91	1	H	20484	0.03
91	2	O	20484	0.03
92	1	H	20249	0.04
92	2	P	20249	0.04
93	1	I	20407	0.04
93	2	J	20407	0.04
94	1	I	20292	0.03
94	2	K	20292	0.03
95	1	I	20210	0.03
95	2	L	20210	0.03
96	1	I	20153	0.05
96	2	M	20153	0.05
97	1	I	20282	0.03
97	2	N	20282	0.03
98	1	I	20413	0.03
98	2	O	20413	0.03
99	1	I	20417	0.04
99	2	P	20417	0.04
100	1	J	20324	0.03
100	2	K	20324	0.03
101	1	J	20239	0.03
101	2	L	20239	0.03
102	1	J	20197	0.05
102	2	M	20197	0.05
103	1	J	20343	0.03
103	2	N	20343	0.03
104	1	J	20389	0.03
104	2	O	20389	0.03
105	1	J	20355	0.04
105	2	P	20355	0.04
106	1	K	20468	0.03
106	2	L	20468	0.03
107	1	K	20292	0.04
107	2	M	20292	0.04
108	1	K	20573	0.03
108	2	N	20573	0.03
109	1	K	20517	0.02
109	2	O	20517	0.02
110	1	K	20353	0.03
110	2	P	20353	0.03
111	1	L	20287	0.05
111	2	M	20287	0.05
112	1	L	20440	0.03
112	2	N	20440	0.03
113	1	L	20399	0.02
113	2	O	20399	0.02
114	1	L	20252	0.03
114	2	P	20252	0.03
115	1	M	20277	0.05
115	2	N	20277	0.05
116	1	M	20337	0.05
116	2	O	20337	0.05
117	1	M	20055	0.05
117	2	P	20055	0.05
118	1	N	20486	0.03
118	2	O	20486	0.03
119	1	N	20357	0.03
119	2	P	20357	0.03
120	1	O	20286	0.03
120	2	P	20286	0.03

LS refinement shell

Resolution: 2.85→2.923 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.359	423	-
Rwork	0.314	8801	-
obs	-	8801	99.2 %

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	1.1477	-0.9691	-0.8535	1.8863	0.1349	2.9945	-0.217	0.0244	0.3725	-0.003	0.1732	0.0181	-0.312	-0.3917	0.0438	0.506	0.1619	-0.2738	0.2515	-0.0605	0.3778	27.8499	16.3131	89.7643
2	0.8305	-0.3739	-0.12	0.8715	-0.3059	0.8197	-0.2001	0.0005	0.3141	-0.0386	0.0826	-0.0983	-0.3193	0.0296	0.1174	0.4631	0.0847	-0.2172	0.2283	-0	0.1868	43.0779	1.5722	85.0999
3	2.9684	0.383	-0.5765	0.9397	0.4019	5.0004	-0.0741	-0.1172	-0.1488	-0.2093	-0.2047	0.3074	-0.1069	-1.0911	0.2788	0.1971	0.2131	-0.1218	0.477	-0.119	0.157	9.2513	-22.9473	96.4908
4	1.3404	0.0635	-0.0453	0.7069	0.3956	2.7714	-0.105	-0.4909	-0.1281	0.068	-0.0469	0.1061	0.0773	-0.6002	0.1519	0.1981	0.2547	-0.085	0.642	-0.0811	0.1209	19.7091	-17.9466	119.5708
5	2.2911	-0.5076	-0.9284	0.7421	-0.1117	3.0947	-0.2045	-0.213	-0.3987	-0.1756	-0.0864	-0.1877	0.3211	0.4785	0.2909	0.2125	0.1711	0.0539	0.1892	0.0335	0.2455	53.7138	-34.714	103.4038
6	0.9442	0.0636	0.0267	0.8742	-0.6971	1.0365	-0.2344	0.0883	-0.0525	-0.1549	0.0448	-0.1185	-0.0036	0.0819	0.1897	0.2658	0.1074	-0.0637	0.1965	-0.0603	0.0714	46.5572	-19.2786	85.2769
7	1.2761	0.6929	-0.6071	0.5532	-0.3287	2.4773	-0.0806	-0.3455	-0.036	0.1408	-0.3195	-0.092	-0.8672	0.0948	0.4001	0.6047	-0.0235	-0.3084	0.2457	-0.0413	0.2252	55.4429	3.9451	123.3083
8	0.703	0.5358	-0.0397	0.637	-0.6432	1.7601	-0.0689	-0.3782	0.2161	0.2069	-0.1015	0.0908	-0.7061	-0.341	0.1703	0.4715	0.3224	-0.1909	0.4948	-0.2359	0.1378	34.8669	-1.3478	124.9481
9	2.4312	0.8501	1.4776	1.1943	0.0843	3.5168	0.1944	-0.3744	-0.3884	0.4427	-0.0425	-0.1453	0.8187	-0.8027	-0.1519	0.4997	-0.1564	-0.0059	0.3344	0.027	0.07	16.1886	-65.0019	51.4532
10	1.3515	0.5996	-0.1796	0.5044	-0.1269	1.5699	0.064	0.0727	-0.3094	0.2701	0.0765	-0.1163	0.1366	0.0043	-0.1405	0.3281	0.0594	-0.0283	0.2469	-0.0184	0.0957	32.0332	-50.6561	47.784
11	5.4294	-0.2409	0.9144	1.5156	0.2051	5.6974	0.3228	-0.7524	0.5737	0.54	-0.4357	0.5615	-0.1077	-0.6189	0.1129	0.5473	-0.016	0.3723	0.3882	-0.1844	0.3386	0.6842	-24.9587	56.4525
12	2.2628	1.1577	0.4272	1.2055	0.533	1.2738	0.0281	0.0892	0.642	0.1582	-0.212	0.6368	-0.2097	-0.5736	0.1838	0.1494	0.1702	0.1344	0.6066	0.0183	0.3678	-6.7259	-30.8426	32.9166
13	3.383	1.3277	1.9522	2.2409	-0.3366	3.9385	-0.1249	0.5381	0.5688	-0.1176	0.1464	0.2405	-0.7628	0.5027	-0.0215	0.6192	-0.0437	0.094	0.4269	0.0475	0.1508	32.1209	-13.6273	27.131
14	1.2424	0.4873	0.7655	0.7823	0.2624	1.3346	0.025	0.0909	0.1163	0.3184	0.1305	0.0345	-0.277	0.2208	-0.1555	0.4464	0.0078	0.0404	0.345	-0.054	0.0753	35.374	-29.7477	46.0145
15	1.9017	-0.3644	-0.1128	1.1761	0.2682	0.7465	-0.1308	0.7331	-0.2897	-0.2444	0.2011	0.0767	0.0151	-0.1916	-0.0703	0.2159	-0.1165	-0.0113	0.6965	-0.1394	0.0744	21.8919	-49.2306	10.8863
16	4.3382	0.0738	0.2884	1.2149	-0.5065	1.2494	-0.1303	0.4971	-0.4866	-0.1212	0.1491	0.3383	0.1244	-0.4096	-0.0188	0.1403	-0.1213	-0.0023	0.6538	-0.0826	0.1784	1.9945	-50.6942	16.3852
17	6.5799	-1.4445	2.11	2.7093	1.8632	2.9939	0.0985	-0.1165	-1.5201	0.3148	0.1762	0.6488	0.5141	0.1725	-0.2747	0.5246	0.1743	0.0026	0.1954	0.0796	0.938	-31.3091	-27.2055	90.966
18	3.7726	-2.1786	0.0665	1.7074	0.2616	1.1819	0.1384	0.3318	-1.5768	-0.1167	-0.0648	1.036	0.3419	-0.2015	-0.0736	0.248	-0.0273	-0.0862	0.211	-0.0489	0.9655	-52.4778	-16.5723	84.8687
19	5.5385	-1.139	2.2162	1.935	-0.0461	4.5045	0.4503	0.9439	1.0125	-0.5452	-0.1233	-0.8822	-0.2274	1.2708	-0.327	0.2491	0.0366	0.3164	0.4886	0.0937	0.6594	-20.7029	13.1996	79.5109
20	3.2681	-1.4535	0.015	0.7886	-0.2292	1.5442	-0.2378	-0.6745	1.0489	0.1868	0.4348	-0.4644	-0.1803	0.4966	-0.1971	0.2157	0.1165	-0.0271	0.6523	-0.3028	0.6676	-18.5977	9.1645	104.1302
21	1.9331	-1.7081	-0.6954	1.9411	0.98	1.7829	-0.1741	-0.5147	-0.1154	0.0364	0.4056	0.0157	-0.2801	-0.2416	-0.2316	0.1481	0.1967	0.0676	0.3631	0.1672	0.2278	-56.409	19.584	105.3212
22	2.3751	-0.6179	-0.6173	2.7407	0.9753	1.6446	-0.0021	0.1229	-0.2355	-0.4128	-0.0563	0.3562	-0.2556	-0.3495	0.0584	0.1707	0.1365	-0.0154	0.217	0.1008	0.2872	-59.4284	10.9672	86.7474
23	6.9399	0.1511	1.2626	1.5902	0.5433	2.1292	-0.8812	-2.6625	-0.9224	0.9768	0.7357	0.5196	0.7045	-0.0381	0.1455	0.9598	0.8274	0.5118	1.5739	0.7498	0.6443	-46.8763	-12.6911	127.5312
24	4.4031	-1.4779	0.4115	1.2235	0.3744	2.0991	-0.6793	-1.4238	-0.3031	0.6077	0.8867	0.1059	0.4453	0.3523	-0.2073	0.3824	0.5342	0.035	0.8315	0.1029	0.2103	-25.7058	-6.5743	117.6596
25	2.1182	-0.0898	-1.5388	1.6455	0.8776	3.619	-0.2977	0.3427	-0.6241	-0.113	-0.0261	0.0809	0.2953	-0.2908	0.3237	0.1827	0.0281	0.0373	0.1326	-0.1075	0.2145	-75.4785	-67.8111	34.1811
26	2.0582	0.0934	-0.2824	2.2881	0.8247	1.4439	-0.0848	0.0988	-0.191	0.05	0.1922	-0.1591	0.1337	-0.0361	-0.1075	0.1941	0.1005	-0.0294	0.1718	0.0439	0.1086	-69.5612	-51.6518	49.7206
27	4.9581	-0.807	-3.6372	1.421	1.0499	6.0461	-0.3036	1.7844	-0.1421	-0.7859	-0.0126	0.4461	-0.4467	-1.2639	0.3162	0.8489	-0.0335	-0.2105	0.9788	0.1429	0.2338	-76.5805	-29.3504	11.4591
28	1.4771	-0.4163	-0.2431	0.8979	0.472	1.9173	-0.0969	0.7137	0.1048	-0.611	0.2506	-0.0795	-0.3255	0.0069	-0.1537	0.733	-0.2259	0.0445	0.8143	0.0108	0.047	-52.5295	-37.0301	9.8436
29	1.8758	0.1845	-0.3223	1.9897	0.1571	0.8099	-0.126	-0.0125	0.4445	-0.0121	0.3782	-0.2906	-0.2277	0.0999	-0.2522	0.2227	0.0454	-0.0103	0.1524	-0.0987	0.1967	-49.2254	-22.121	45.7975
30	2.3749	1.2022	-0.5203	2.2327	0.1924	2.0453	-0.0593	-0.0205	0.3936	0.0707	0.302	0.0937	-0.2135	-0.137	-0.2427	0.2597	0.1611	-0.0011	0.1811	0.0497	0.1724	-68.638	-27.955	50.1804
31	2.1523	-0.3395	-1.4996	1.6108	0.2079	7.0619	-0.0367	-0.1162	-0.3716	0.1907	0.4155	-0.3957	-0.0734	1.3699	-0.3788	0.129	0.0914	-0.0963	0.4331	-0.2693	0.2985	-34.5484	-58.3548	45.8847
32	1.68	-0.0424	-0.3903	0.7072	0.2047	2.6498	0.079	0.4108	-0.2033	-0.4058	0.271	-0.234	-0.0831	0.6353	-0.35	0.2459	-0.0813	0.1069	0.6069	-0.2968	0.1685	-37.0203	-53.9144	21.0566

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 169
2	X-RAY DIFFRACTION	2	A	170 - 331
3	X-RAY DIFFRACTION	3	B	0 - 129
4	X-RAY DIFFRACTION	4	B	130 - 331
5	X-RAY DIFFRACTION	5	C	1 - 153
6	X-RAY DIFFRACTION	6	C	154 - 331
7	X-RAY DIFFRACTION	7	D	1 - 171
8	X-RAY DIFFRACTION	8	D	172 - 331
9	X-RAY DIFFRACTION	9	E	1 - 169
10	X-RAY DIFFRACTION	10	E	170 - 331
11	X-RAY DIFFRACTION	11	F	1 - 101
12	X-RAY DIFFRACTION	12	F	102 - 331
13	X-RAY DIFFRACTION	13	G	1 - 151
14	X-RAY DIFFRACTION	14	G	152 - 331
15	X-RAY DIFFRACTION	15	H	1 - 206
16	X-RAY DIFFRACTION	16	H	207 - 331
17	X-RAY DIFFRACTION	17	I	2 - 83
18	X-RAY DIFFRACTION	18	I	84 - 331
19	X-RAY DIFFRACTION	19	J	2 - 143
20	X-RAY DIFFRACTION	20	J	144 - 331
21	X-RAY DIFFRACTION	21	K	1 - 206
22	X-RAY DIFFRACTION	22	K	207 - 331
23	X-RAY DIFFRACTION	23	L	1 - 158
24	X-RAY DIFFRACTION	24	L	159 - 331
25	X-RAY DIFFRACTION	25	M	1 - 163
26	X-RAY DIFFRACTION	26	M	164 - 331
27	X-RAY DIFFRACTION	27	N	1 - 145
28	X-RAY DIFFRACTION	28	N	146 - 331
29	X-RAY DIFFRACTION	29	O	1 - 207
30	X-RAY DIFFRACTION	30	O	208 - 331
31	X-RAY DIFFRACTION	31	P	2 - 101
32	X-RAY DIFFRACTION	32	P	102 - 331