PDB-2b3y: Structure of a monoclinic crystal form of human cytosolic aconita...

Basic information

• Entry: Database: PDB / ID: 2b3y
• Title: Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)
• Components: Iron-responsive element binding protein 1
• Keywords: LYASE / IRP1 IRE-IRP1 aconitase activity

Function / homology

Function:

aconitate hydratase / aconitate hydratase activity / iron-responsive element binding / NADPH regeneration / citrate metabolic process / NADPH regeneration / intestinal absorption / 3 iron, 4 sulfur cluster binding / response to iron(II) ion / iron-sulfur cluster binding / tricarboxylic acid cycle / mRNA regulatory element binding translation repressor activity / post-embryonic development / Iron uptake and transport / 4 iron, 4 sulfur cluster binding / intracellular iron ion homeostasis / endoplasmic reticulum / Golgi apparatus / mitochondrion / RNA binding / extracellular exosome / metal ion binding / cytosol / cytoplasm

Domain/homology:

Apolipoprotein Cii; Chain: A; / Apolipoprotein Cii; Chain: A; - #10 / Aconitase/Iron-responsive element-binding protein 2 / Aconitase A, swivel domain / Aconitase; Domain 2 / Aconitase, Domain 2 / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain / Aconitase family (aconitate hydratase) / Aconitase family signature 1. / Aconitase family signature 2. / Aconitase; domain 4 / Aconitase, domain 4 / Aconitase A/isopropylmalate dehydratase small subunit, swivel domain / Aconitase C-terminal domain / Aconitase/3-isopropylmalate dehydratase, swivel / Helix non-globular / Special / Alpha-Beta Barrel / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ACETATE ION / FORMIC ACID / IRON/SULFUR CLUSTER / Cytoplasmic aconitate hydratase

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
• Authors: Dupuy, J. / Fontecilla-Camps, J.C. / Volbeda, A.

Citation

Journal: Structure / Year: 2006
Title: Crystal structure of human iron regulatory protein 1 as cytosolic aconitase
Authors: Dupuy, J. / Volbeda, A. / Carpentier, P. / Darnault, C. / Moulis, J.M. / Fontecilla-Camps, J.C.

#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and Preliminary X-Ray Diffraction Data For the Aconitase Form of Human Iron Regulatory Protein 1
Authors: Dupuy, J. / DARNAULT, C. / BRAZZOLOTTO, X. / KUHN, L.C. / MOULIS, J.M. / Volbeda, A. / Fontecilla-Camps, J.C.

History

Deposition	Sep 22, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 10, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.3	Aug 23, 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_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_atom_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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Iron-responsive element binding protein 1

B: Iron-responsive element binding protein 1

hetero molecules

Summary:

• 198 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	197,859	10
Polymers	196,749	2
Non-polymers	1,111	8
Water	17,475	970

1

A: Iron-responsive element binding protein 1

hetero molecules

Summary:

• defined by author
• 99 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,969	5
Polymers	98,374	1
Non-polymers	595	4
Water	18	1

Symmetry operations:

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

2

B: Iron-responsive element binding protein 1

hetero molecules

Summary:

• defined by author
• 98.9 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	98,890	5
Polymers	98,374	1
Non-polymers	516	4
Water	18	1

Symmetry operations:

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

Unit cell

Length a, b, c (Å)	63.910, 215.470, 64.010
Angle α, β, γ (deg.)	90.00, 72.00, 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
3	1	A
4	1	B
5	1	A
6	1	B
7	1	A
8	1	B
9	1	A
10	1	B
11	1	A
12	1	B
13	1	A
14	1	B
15	1	A
16	1	B
17	1	A
18	1	B
19	1	A
20	1	B
21	1	A
22	1	B
23	1	A
24	1	B
25	1	A
26	1	B
27	1	A
28	1	B
29	1	A
30	1	B
31	1	A
32	1	B
33	1	A
34	1	B
1	2	A
2	2	B
3	2	A
4	2	B
5	2	A
6	2	B
7	2	A
8	2	B
9	2	A
10	2	B
11	2	A
12	2	B
13	2	A
14	2	B
15	2	A
16	2	B
17	2	A
18	2	B
19	2	A
20	2	B
21	2	A
22	2	B
23	2	A
24	2	B
25	2	A
26	2	B
27	2	A
28	2	B
29	2	A
30	2	B
31	2	A
32	2	B
33	2	A
34	2	B
35	2	A
36	2	B
37	2	A
38	2	B
39	2	A
40	2	B
41	2	A
42	2	B
43	2	A
44	2	B
45	2	A
46	2	B
47	2	A
48	2	B
49	2	A
50	2	B
51	2	A
52	2	B
1	3	A
2	3	B
3	3	A
4	3	B
5	3	A
6	3	B
7	3	A
8	3	B
9	3	A
10	3	B
11	3	A
12	3	B
13	3	A
14	3	B
15	3	A
16	3	B
17	3	A
18	3	B
19	3	A
20	3	B
21	3	A
22	3	B
23	3	A
24	3	B
25	3	A
26	3	B
27	3	A
28	3	B
29	3	A
30	3	B
31	3	A
32	3	B
33	3	A
34	3	B
35	3	A
36	3	B
37	3	A
38	3	B
39	3	A
40	3	B
41	3	A
42	3	B
43	3	A
44	3	B
45	3	A
46	3	B
47	3	A
48	3	B
1	4	A
2	4	B
3	4	A
4	4	B
5	4	A
6	4	B
7	4	A
8	4	B
9	4	A
10	4	B
11	4	A
12	4	B
13	4	A
14	4	B
15	4	A
16	4	B
17	4	A
18	4	B
19	4	A
20	4	B
21	4	A
22	4	B
23	4	A
24	4	B
25	4	A
26	4	B
27	4	A
28	4	B
29	4	A
30	4	B
31	4	A
32	4	B
33	4	A
34	4	B
35	4	A
36	4	B
37	4	A
38	4	B
39	4	A
40	4	B
41	4	A
42	4	B
43	4	A
44	4	B
45	4	A
46	4	B
47	4	A
48	4	B
49	4	A
50	4	B
51	4	A
52	4	B
53	4	A
54	4	B
55	4	A
56	4	B
57	4	A
58	4	B
59	4	A
60	4	B
61	4	A
62	4	B
63	4	A
64	4	B
65	4	A
66	4	B
67	4	A
68	4	B
69	4	A
70	4	B
71	4	A
72	4	B
73	4	A
74	4	B
75	4	A
76	4	B
77	4	A
78	4	B
79	4	A
80	4	B
1	5	A
2	5	B
3	5	A
4	5	B
5	5	A
6	5	B
7	5	A
8	5	B
9	5	A
10	5	B
11	5	A
12	5	B
13	5	A
14	5	B
15	5	A
16	5	B
17	5	A
18	5	B
19	5	A
20	5	B
21	5	A
22	5	B
23	5	A
24	5	B
25	5	A
26	5	B
27	5	A
28	5	B
29	5	A
30	5	B
31	5	A
32	5	B
33	5	A
34	5	B
1	6	A
2	6	B
3	6	A
4	6	B
5	6	A
6	6	B
7	6	A
8	6	B
9	6	A
10	6	B
11	6	A
12	6	B
13	6	A
14	6	B
15	6	A
16	6	B
17	6	A
18	6	B
19	6	A
20	6	B
21	6	A
22	6	B
23	6	A
24	6	B
25	6	A
26	6	B
27	6	A
28	6	B
29	6	A
30	6	B
31	6	A
32	6	B
33	6	A
34	6	B
35	6	A
36	6	B
37	6	A
38	6	B
39	6	A
40	6	B
41	6	A
42	6	B
43	6	A
44	6	B
45	6	A
46	6	B
47	6	A
48	6	B
49	6	A
50	6	B
51	6	A
52	6	B
53	6	A
54	6	B
55	6	A
56	6	B
57	6	A
58	6	B
59	6	A
60	6	B
61	6	A
62	6	B
63	6	A
64	6	B
65	6	A
66	6	B
67	6	A
68	6	B
69	6	A
70	6	B
71	6	A
72	6	B
73	6	A
74	6	B
75	6	A
76	6	B
77	6	A
78	6	B
79	6	A
80	6	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	SER	SER	6	A	A	2	1
2	1	1	SER	SER	SER	SER	6	B	B	2	1
3	2	1	ASN	ASN	PRO	PRO	2	A	A	3 - 4	2 - 3
4	2	1	ASN	ASN	PRO	PRO	2	B	B	3 - 4	2 - 3
5	3	1	PHE	PHE	ALA	ALA	1	A	A	5 - 6	4 - 5
6	3	1	PHE	PHE	ALA	ALA	1	B	B	5 - 6	4 - 5
7	4	1	HIS	HIS	HIS	HIS	2	A	A	7	6
8	4	1	HIS	HIS	HIS	HIS	2	B	B	7	6
9	5	1	LEU	LEU	PRO	PRO	1	A	A	8 - 11	7 - 10
10	5	1	LEU	LEU	PRO	PRO	1	B	B	8 - 11	7 - 10
11	6	1	LEU	LEU	ASP	ASP	2	A	A	12 - 13	11 - 12
12	6	1	LEU	LEU	ASP	ASP	2	B	B	12 - 13	11 - 12
13	7	1	PRO	PRO	VAL	VAL	1	A	A	14 - 15	13 - 14
14	7	1	PRO	PRO	VAL	VAL	1	B	B	14 - 15	13 - 14
15	8	1	GLN	GLN	LYS	LYS	2	A	A	16 - 20	15 - 19
16	8	1	GLN	GLN	LYS	LYS	2	B	B	16 - 20	15 - 19
17	9	1	PHE	PHE	ASN	ASN	1	A	A	21 - 25	20 - 24
18	9	1	PHE	PHE	ASN	ASN	1	B	B	21 - 25	20 - 24
19	10	1	LYS	LYS	GLU	GLU	2	A	A	26 - 28	25 - 27
20	10	1	LYS	LYS	GLU	GLU	2	B	B	26 - 28	25 - 27
21	11	1	ASP	ASP	VAL	VAL	1	A	A	29 - 41	28 - 40
22	11	1	ASP	ASP	VAL	VAL	1	B	B	29 - 41	28 - 40
23	12	1	LEU	LEU	LEU	LEU	2	A	A	42	41
24	12	1	LEU	LEU	LEU	LEU	2	B	B	42	41
25	13	1	LEU	LEU	ASP	ASP	1	A	A	43 - 51	42 - 50
26	13	1	LEU	LEU	ASP	ASP	1	B	B	43 - 51	42 - 50
27	14	1	GLU	GLU	GLN	GLN	2	A	A	52 - 58	51 - 57
28	14	1	GLU	GLU	GLN	GLN	2	B	B	52 - 58	51 - 57
29	15	1	ASP	ASP	HIS	HIS	1	A	A	59 - 71	58 - 70
30	15	1	ASP	ASP	HIS	HIS	1	B	B	59 - 71	58 - 70
31	16	1	LYS	LYS	ASN	ASN	2	A	A	72 - 73	71 - 72
32	16	1	LYS	LYS	ASN	ASN	2	B	B	72 - 73	71 - 72
33	17	1	ILE	ILE	ILE	ILE	1	A	A	74	73
34	17	1	ILE	ILE	ILE	ILE	1	B	B	74	73
1	1	2	GLU	GLU	PHE	PHE	1	A	A	75 - 78	74 - 77
2	1	2	GLU	GLU	PHE	PHE	1	B	B	75 - 78	74 - 77
3	2	2	LYS	LYS	LYS	LYS	2	A	A	79	78
4	2	2	LYS	LYS	LYS	LYS	2	B	B	79	78
5	3	2	PRO	PRO	PHE	PHE	1	A	A	80 - 88	79 - 87
6	3	2	PRO	PRO	PHE	PHE	1	B	B	80 - 88	79 - 87
7	4	2	THR	THR	THR	THR	2	A	A	89	88
8	4	2	THR	THR	THR	THR	2	B	B	89	88
9	5	2	GLY	GLY	VAL	VAL	1	A	A	90 - 104	89 - 103
10	5	2	GLY	GLY	VAL	VAL	1	B	B	90 - 104	89 - 103
11	6	2	LYS	LYS	LYS	LYS	2	A	A	105 - 113	104 - 112
12	6	2	LYS	LYS	LYS	LYS	2	B	B	105 - 113	104 - 112
13	7	2	ILE	ILE	GLN	GLN	1	A	A	114 - 129	113 - 128
14	7	2	ILE	ILE	GLN	GLN	1	B	B	114 - 129	113 - 128
15	8	2	VAL	VAL	ARG	ARG	2	A	A	130 - 135	129 - 134
16	8	2	VAL	VAL	ARG	ARG	2	B	B	130 - 135	129 - 134
17	9	2	ALA	ALA	ASP	ASP	1	A	A	136 - 137	135 - 136
18	9	2	ALA	ALA	ASP	ASP	1	B	B	136 - 137	135 - 136
19	10	2	SER	SER	LYS	LYS	2	A	A	138 - 141	137 - 140
20	10	2	SER	SER	LYS	LYS	2	B	B	138 - 141	137 - 140
21	11	2	ASN	ASN	GLN	GLN	1	A	A	142 - 143	141 - 142
22	11	2	ASN	ASN	GLN	GLN	1	B	B	142 - 143	141 - 142
23	12	2	ASP	ASP	ASP	ASP	2	A	A	144	143
24	12	2	ASP	ASP	ASP	ASP	2	B	B	144	143
25	13	2	LEU	LEU	PHE	PHE	1	A	A	145 - 147	144 - 146
26	13	2	LEU	LEU	PHE	PHE	1	B	B	145 - 147	144 - 146
27	14	2	GLU	GLU	GLU	GLU	2	A	A	148	147
28	14	2	GLU	GLU	GLU	GLU	2	B	B	148	147
29	15	2	ARG	ARG	ASN	ASN	1	A	A	149 - 150	148 - 149
30	15	2	ARG	ARG	ASN	ASN	1	B	B	149 - 150	148 - 149
31	16	2	ARG	ARG	ARG	ARG	2	A	A	151	150
32	16	2	ARG	ARG	ARG	ARG	2	B	B	151	150
33	17	2	GLU	GLU	MET	MET	1	A	A	152 - 167	151 - 166
34	17	2	GLU	GLU	MET	MET	1	B	B	152 - 167	151 - 166
35	18	2	ARG	ARG	ILE	ILE	2	A	A	168 - 170	167 - 169
36	18	2	ARG	ARG	ILE	ILE	2	B	B	168 - 170	167 - 169
37	19	2	PRO	PRO	GLN	GLN	1	A	A	171 - 192	170 - 191
38	19	2	PRO	PRO	GLN	GLN	1	B	B	171 - 192	170 - 191
39	20	2	ASP	ASP	TYR	TYR	2	A	A	193 - 195	192 - 194
40	20	2	ASP	ASP	TYR	TYR	2	B	B	193 - 195	192 - 194
41	21	2	TYR	TYR	SER	SER	1	A	A	196 - 200	195 - 199
42	21	2	TYR	TYR	SER	SER	1	B	B	196 - 200	195 - 199
43	22	2	LEU	LEU	VAL	VAL	2	A	A	201 - 202	200 - 201
44	22	2	LEU	LEU	VAL	VAL	2	B	B	201 - 202	200 - 201
45	23	2	GLY	GLY	MET	MET	1	A	A	203 - 210	202 - 209
46	23	2	GLY	GLY	MET	MET	1	B	B	203 - 210	202 - 209
47	24	2	ILE	ILE	ILE	ILE	2	A	A	211	210
48	24	2	ILE	ILE	ILE	ILE	2	B	B	211	210
49	25	2	ASP	ASP	LEU	LEU	1	A	A	212 - 239	211 - 238
50	25	2	ASP	ASP	LEU	LEU	1	B	B	212 - 239	211 - 238
51	26	2	PRO	PRO	PRO	PRO	2	A	A	240	239
52	26	2	PRO	PRO	PRO	PRO	2	B	B	240	239
1	1	3	GLN	GLN	GLN	GLN	2	A	A	241	240
2	1	3	GLN	GLN	GLN	GLN	2	B	B	241	240
3	2	3	VAL	VAL	LEU	LEU	1	A	A	242 - 247	241 - 246
4	2	3	VAL	VAL	LEU	LEU	1	B	B	242 - 247	241 - 246
5	3	3	MET	MET	LYS	LYS	2	A	A	248 - 250	247 - 249
6	3	3	MET	MET	LYS	LYS	2	B	B	248 - 250	247 - 249
7	4	3	PRO	PRO	ASP	ASP	1	A	A	251 - 259	250 - 258
8	4	3	PRO	PRO	ASP	ASP	1	B	B	251 - 259	250 - 258
9	5	3	ILE	ILE	ILE	ILE	2	A	A	260	259
10	5	3	ILE	ILE	ILE	ILE	2	B	B	260	259
11	6	3	VAL	VAL	ALA	ALA	1	A	A	261 - 286	260 - 285
12	6	3	VAL	VAL	ALA	ALA	1	B	B	261 - 286	260 - 285
13	7	3	GLN	GLN	GLN	GLN	2	A	A	287	286
14	7	3	GLN	GLN	GLN	GLN	2	B	B	287	286
15	8	3	LEU	LEU	VAL	VAL	1	A	A	288 - 321	287 - 320
16	8	3	LEU	LEU	VAL	VAL	1	B	B	288 - 321	287 - 320
17	9	3	GLN	GLN	THR	THR	2	A	A	322 - 323	321 - 322
18	9	3	GLN	GLN	THR	THR	2	B	B	322 - 323	321 - 322
19	10	3	GLY	GLY	ARG	ARG	1	A	A	324 - 325	323 - 324
20	10	3	GLY	GLY	ARG	ARG	1	B	B	324 - 325	323 - 324
21	11	3	ASP	ASP	LYS	LYS	2	A	A	326 - 329	325 - 328
22	11	3	ASP	ASP	LYS	LYS	2	B	B	326 - 329	325 - 328
23	12	3	LEU	LEU	ILE	ILE	1	A	A	330 - 333	329 - 332
24	12	3	LEU	LEU	ILE	ILE	1	B	B	330 - 333	329 - 332
25	13	3	LYS	LYS	LYS	LYS	2	A	A	334 - 335	333 - 334
26	13	3	LYS	LYS	LYS	LYS	2	B	B	334 - 335	333 - 334
27	14	3	TYR	TYR	LEU	LEU	1	A	A	336 - 337	335 - 336
28	14	3	TYR	TYR	LEU	LEU	1	B	B	336 - 337	335 - 336
29	15	3	GLN	GLN	GLN	GLN	4	A	A	338	337
30	15	3	GLN	GLN	GLN	GLN	4	B	B	338	337
31	16	3	ALA	ALA	PHE	PHE	1	A	A	339 - 346	338 - 345
32	16	3	ALA	ALA	PHE	PHE	1	B	B	339 - 346	338 - 345
33	17	3	ASN	ASN	ASN	ASN	2	A	A	347	346
34	17	3	ASN	ASN	ASN	ASN	2	B	B	347	346
35	18	3	ASP	ASP	ASP	ASP	1	A	A	348	347
36	18	3	ASP	ASP	ASP	ASP	1	B	B	348	347
37	19	3	PRO	PRO	PRO	PRO	2	A	A	349	348
38	19	3	PRO	PRO	PRO	PRO	2	B	B	349	348
39	20	3	SER	SER	PRO	PRO	1	A	A	350 - 353	349 - 352
40	20	3	SER	SER	PRO	PRO	1	B	B	350 - 353	349 - 352
41	21	3	ASP	ASP	ASP	ASP	2	A	A	354	353
42	21	3	ASP	ASP	ASP	ASP	2	B	B	354	353
43	22	3	PHE	PHE	THR	THR	1	A	A	355 - 356	354 - 355
44	22	3	PHE	PHE	THR	THR	1	B	B	355 - 356	354 - 355
45	23	3	GLN	GLN	GLN	GLN	2	A	A	357	356
46	23	3	GLN	GLN	GLN	GLN	2	B	B	357	356
47	24	3	VAL	VAL	VAL	VAL	1	A	A	358 - 366	357 - 365
48	24	3	VAL	VAL	VAL	VAL	1	B	B	358 - 366	357 - 365
1	1	4	PRO	PRO	PRO	PRO	2	A	A	368	367
2	1	4	PRO	PRO	PRO	PRO	2	B	B	368	367
3	2	4	CYS	CYS	PRO	PRO	1	A	A	369 - 373	368 - 372
4	2	4	CYS	CYS	PRO	PRO	1	B	B	369 - 373	368 - 372
5	3	4	LYS	LYS	LYS	LYS	2	A	A	374 - 379	373 - 378
6	3	4	LYS	LYS	LYS	LYS	2	B	B	374 - 379	373 - 378
7	4	4	VAL	VAL	VAL	VAL	1	A	A	380 - 382	379 - 381
8	4	4	VAL	VAL	VAL	VAL	1	B	B	380 - 382	379 - 381
9	5	4	SER	SER	SER	SER	2	A	A	383 - 391	382 - 390
10	5	4	SER	SER	SER	SER	2	B	B	383 - 391	382 - 390
11	6	4	CYS	CYS	ALA	ALA	1	A	A	392 - 395	391 - 394
12	6	4	CYS	CYS	ALA	ALA	1	B	B	392 - 395	391 - 394
13	7	4	LYS	LYS	GLN	GLN	2	A	A	396 - 397	395 - 396
14	7	4	LYS	LYS	GLN	GLN	2	B	B	396 - 397	395 - 396
15	8	4	GLY	GLY	PHE	PHE	1	A	A	398 - 402	397 - 401
16	8	4	GLY	GLY	PHE	PHE	1	B	B	398 - 402	397 - 401
17	9	4	GLN	GLN	GLN	GLN	2	A	A	403	402
18	9	4	GLN	GLN	GLN	GLN	2	B	B	403	402
19	10	4	VAL	VAL	PRO	PRO	1	A	A	404 - 406	403 - 405
20	10	4	VAL	VAL	PRO	PRO	1	B	B	404 - 406	403 - 405
21	11	4	GLU	GLU	LEU	LEU	2	A	A	407 - 424	406 - 423
22	11	4	GLU	GLU	LEU	LEU	2	B	B	407 - 424	406 - 423
23	12	4	ALA	ALA	GLY	GLY	1	A	A	425 - 427	424 - 426
24	12	4	ALA	ALA	GLY	GLY	1	B	B	425 - 427	424 - 426
25	13	4	SER	SER	SER	SER	2	A	A	428	427
26	13	4	SER	SER	SER	SER	2	B	B	428	427
27	14	4	VAL	VAL	ALA	ALA	1	A	A	429 - 433	428 - 432
28	14	4	VAL	VAL	ALA	ALA	1	B	B	429 - 433	428 - 432
29	15	4	ILE	ILE	SER	SER	2	A	A	434 - 436	433 - 435
30	15	4	ILE	ILE	SER	SER	2	B	B	434 - 436	433 - 435
31	16	4	CYS	CYS	GLY	GLY	1	A	A	437 - 450	436 - 449
32	16	4	CYS	CYS	GLY	GLY	1	B	B	437 - 450	436 - 449
33	17	4	LEU	LEU	LYS	LYS	2	A	A	451 - 455	450 - 454
34	17	4	LEU	LEU	LYS	LYS	2	B	B	451 - 455	450 - 454
35	18	4	ALA	ALA	LEU	LEU	1	A	A	456 - 461	455 - 460
36	18	4	ALA	ALA	LEU	LEU	1	B	B	456 - 461	455 - 460
37	19	4	ASN	ASN	MET	MET	2	A	A	462 - 464	461 - 463
38	19	4	ASN	ASN	MET	MET	2	B	B	462 - 464	461 - 463
39	20	4	PRO	PRO	ILE	ILE	1	A	A	465 - 467	464 - 466
40	20	4	PRO	PRO	ILE	ILE	1	B	B	465 - 467	464 - 466
41	21	4	LYS	LYS	LYS	LYS	2	A	A	468	467
42	21	4	LYS	LYS	LYS	LYS	2	B	B	468	467
43	22	4	THR	THR	LEU	LEU	1	A	A	469 - 482	468 - 481
44	22	4	THR	THR	LEU	LEU	1	B	B	469 - 482	468 - 481
45	23	4	GLN	GLN	MET	MET	2	A	A	483 - 488	482 - 487
46	23	4	GLN	GLN	MET	MET	2	B	B	483 - 488	482 - 487
47	24	4	PRO	PRO	SER	SER	1	A	A	489 - 492	488 - 491
48	24	4	PRO	PRO	SER	SER	1	B	B	489 - 492	488 - 491
49	25	4	GLN	GLN	GLN	GLN	2	A	A	493	492
50	25	4	GLN	GLN	GLN	GLN	2	B	B	493	492
51	26	4	LEU	LEU	CYS	CYS	1	A	A	494 - 506	493 - 505
52	26	4	LEU	LEU	CYS	CYS	1	B	B	494 - 506	493 - 505
53	27	4	ILE	ILE	ILE	ILE	2	A	A	507	506
54	27	4	ILE	ILE	ILE	ILE	2	B	B	507	506
55	28	4	GLY	GLY	PRO	PRO	1	A	A	508 - 512	507 - 511
56	28	4	GLY	GLY	PRO	PRO	1	B	B	508 - 512	507 - 511
57	29	4	LEU	LEU	GLU	GLU	2	A	A	513 - 515	512 - 514
58	29	4	LEU	LEU	GLU	GLU	2	B	B	513 - 515	512 - 514
59	30	4	PRO	PRO	VAL	VAL	1	A	A	516 - 518	515 - 517
60	30	4	PRO	PRO	VAL	VAL	1	B	B	516 - 518	515 - 517
61	31	4	GLU	GLU	ASP	ASP	2	A	A	519 - 525	518 - 524
62	31	4	GLU	GLU	ASP	ASP	2	B	B	519 - 525	518 - 524
63	32	4	LEU	LEU	ASN	ASN	1	A	A	526 - 535	525 - 534
64	32	4	LEU	LEU	ASN	ASN	1	B	B	526 - 535	525 - 534
65	33	4	ARG	ARG	PHE	PHE	2	A	A	536 - 538	535 - 537
66	33	4	ARG	ARG	PHE	PHE	2	B	B	536 - 538	535 - 537
67	34	4	GLU	GLU	ARG	ARG	5	A	A	539 - 547	538 - 546
68	34	4	GLU	GLU	ARG	ARG	5	B	B	539 - 547	538 - 546
69	35	4	ALA	ALA	VAL	VAL	1	A	A	548 - 557	547 - 556
70	35	4	ALA	ALA	VAL	VAL	1	B	B	548 - 557	547 - 556
71	36	4	ILE	ILE	ILE	ILE	2	A	A	558	557
72	36	4	ILE	ILE	ILE	ILE	2	B	B	558	557
73	37	4	ALA	ALA	ILE	ILE	1	A	A	559 - 568	558 - 567
74	37	4	ALA	ALA	ILE	ILE	1	B	B	559 - 568	558 - 567
75	38	4	ASP	ASP	GLU	GLU	2	A	A	569 - 573	568 - 572
76	38	4	ASP	ASP	GLU	GLU	2	B	B	569 - 573	568 - 572
77	39	4	PRO	PRO	GLY	GLY	1	A	A	574 - 576	573 - 575
78	39	4	PRO	PRO	GLY	GLY	1	B	B	574 - 576	573 - 575
79	40	4	VAL	VAL	TRP	TRP	2	A	A	577 - 590	576 - 589
80	40	4	VAL	VAL	TRP	TRP	2	B	B	577 - 590	576 - 589
1	1	5	PRO	PRO	THR	THR	1	A	A	591 - 592	590 - 591
2	1	5	PRO	PRO	THR	THR	1	B	B	591 - 592	590 - 591
3	2	5	ARG	ARG	GLU	GLU	2	A	A	593 - 595	592 - 594
4	2	5	ARG	ARG	GLU	GLU	2	B	B	593 - 595	592 - 594
5	3	5	ILE	ILE	ILE	ILE	1	A	A	596	595
6	3	5	ILE	ILE	ILE	ILE	1	B	B	596	595
7	4	5	GLN	GLN	GLN	GLN	2	A	A	597	596
8	4	5	GLN	GLN	GLN	GLN	2	B	B	597	596
9	5	5	ALA	ALA	GLU	GLU	4	A	A	598 - 600	597 - 599
10	5	5	ALA	ALA	GLU	GLU	4	B	B	598 - 600	597 - 599
11	6	5	ARG	ARG	GLN	GLN	5	A	A	601 - 602	600 - 601
12	6	5	ARG	ARG	GLN	GLN	5	B	B	601 - 602	600 - 601
13	7	5	TYR	TYR	ILE	ILE	4	A	A	603 - 605	602 - 604
14	7	5	TYR	TYR	ILE	ILE	4	B	B	603 - 605	602 - 604
15	8	5	PRO	PRO	LYS	LYS	5	A	A	606 - 610	605 - 609
16	8	5	PRO	PRO	LYS	LYS	5	B	B	606 - 610	605 - 609
17	9	5	GLU	GLU	TYR	TYR	4	A	A	611 - 613	610 - 612
18	9	5	GLU	GLU	TYR	TYR	4	B	B	611 - 613	610 - 612
19	10	5	GLN	GLN	LEU	LEU	2	A	A	614 - 626	613 - 625
20	10	5	GLN	GLN	LEU	LEU	2	B	B	614 - 626	613 - 625
21	11	5	ALA	ALA	ASP	ASP	1	A	A	627 - 631	626 - 630
22	11	5	ALA	ALA	ASP	ASP	1	B	B	627 - 631	626 - 630
23	12	5	LYS	LYS	PHE	PHE	2	A	A	632 - 635	631 - 634
24	12	5	LYS	LYS	PHE	PHE	2	B	B	632 - 635	631 - 634
25	13	5	TRP	TRP	TRP	TRP	1	A	A	636	635
26	13	5	TRP	TRP	TRP	TRP	1	B	B	636	635
27	14	5	ASN	ASN	LYS	LYS	2	A	A	637 - 639	636 - 638
28	14	5	ASN	ASN	LYS	LYS	2	B	B	637 - 639	636 - 638
29	15	5	SER	SER	PHE	PHE	1	A	A	640 - 649	639 - 648
30	15	5	SER	SER	PHE	PHE	1	B	B	640 - 649	639 - 648
31	16	5	GLU	GLU	ASN	ASN	2	A	A	650 - 651	649 - 650
32	16	5	GLU	GLU	ASN	ASN	2	B	B	650 - 651	649 - 650
33	17	5	LEU	LEU	THR	THR	1	A	A	652 - 653	651 - 652
34	17	5	LEU	LEU	THR	THR	1	B	B	652 - 653	651 - 652
1	1	6	LEU	LEU	ILE	ILE	2	A	A	654 - 662	653 - 661
2	1	6	LEU	LEU	ILE	ILE	2	B	B	654 - 662	653 - 661
3	2	6	VAL	VAL	TYR	TYR	1	A	A	663 - 666	662 - 665
4	2	6	VAL	VAL	TYR	TYR	1	B	B	663 - 666	662 - 665
5	3	6	VAL	VAL	ASN	ASN	2	A	A	667 - 670	666 - 669
6	3	6	VAL	VAL	ASN	ASN	2	B	B	667 - 670	666 - 669
7	4	6	LEU	LEU	THR	THR	1	A	A	671 - 676	670 - 675
8	4	6	LEU	LEU	THR	THR	1	B	B	671 - 676	670 - 675
9	5	6	THR	THR	ASP	ASP	2	A	A	677 - 678	676 - 677
10	5	6	THR	THR	ASP	ASP	2	B	B	677 - 678	676 - 677
11	6	6	HIS	HIS	GLY	GLY	1	A	A	679 - 684	678 - 683
12	6	6	HIS	HIS	GLY	GLY	1	B	B	679 - 684	678 - 683
13	7	6	ASN	ASN	ASN	ASN	2	A	A	685 - 689	684 - 688
14	7	6	ASN	ASN	ASN	ASN	2	B	B	685 - 689	684 - 688
15	8	6	SER	SER	THR	THR	1	A	A	690 - 697	689 - 696
16	8	6	SER	SER	THR	THR	1	B	B	690 - 697	689 - 696
17	9	6	ASN	ASN	ARG	ARG	2	A	A	698 - 699	697 - 698
18	9	6	ASN	ASN	ARG	ARG	2	B	B	698 - 699	697 - 698
19	10	6	GLY	GLY	PRO	PRO	1	A	A	700 - 703	699 - 702
20	10	6	GLY	GLY	PRO	PRO	1	B	B	700 - 703	699 - 702
21	11	6	ARG	ARG	GLU	GLU	2	A	A	704 - 705	703 - 704
22	11	6	ARG	ARG	GLU	GLU	2	B	B	704 - 705	703 - 704
23	12	6	PHE	PHE	GLY	GLY	1	A	A	706 - 710	705 - 709
24	12	6	PHE	PHE	GLY	GLY	1	B	B	706 - 710	705 - 709
25	13	6	SER	SER	SER	SER	2	A	A	711	710
26	13	6	SER	SER	SER	SER	2	B	B	711	710
27	14	6	ARG	ARG	ASN	ASN	1	A	A	712 - 731	711 - 730
28	14	6	ARG	ARG	ASN	ASN	1	B	B	712 - 731	711 - 730
29	15	6	ARG	ARG	GLN	GLN	2	A	A	732 - 740	731 - 739
30	15	6	ARG	ARG	GLN	GLN	2	B	B	732 - 740	731 - 739
31	16	6	THR	THR	SER	SER	1	A	A	741 - 746	740 - 745
32	16	6	THR	THR	SER	SER	1	B	B	741 - 746	740 - 745
33	17	6	GLY	GLY	ILE	ILE	2	A	A	747 - 749	746 - 748
34	17	6	GLY	GLY	ILE	ILE	2	B	B	747 - 749	746 - 748
35	18	6	LEU	LEU	ALA	ALA	1	A	A	750 - 756	749 - 755
36	18	6	LEU	LEU	ALA	ALA	1	B	B	750 - 756	749 - 755
37	19	6	GLU	GLU	GLN	GLN	2	A	A	757 - 761	756 - 760
38	19	6	GLU	GLU	GLN	GLN	2	B	B	757 - 761	756 - 760
39	20	6	ALA	ALA	GLY	GLY	1	A	A	762 - 771	761 - 770
40	20	6	ALA	ALA	GLY	GLY	1	B	B	762 - 771	761 - 770
41	21	6	LYS	LYS	LYS	LYS	2	A	A	772	771
42	21	6	LYS	LYS	LYS	LYS	2	B	B	772	771
43	22	6	GLU	GLU	GLY	GLY	1	A	A	773 - 777	772 - 776
44	22	6	GLU	GLU	GLY	GLY	1	B	B	773 - 777	772 - 776
45	23	6	SER	SER	SER	SER	2	A	A	778	777
46	23	6	SER	SER	SER	SER	2	B	B	778	777
47	24	6	SER	SER	ILE	ILE	1	A	A	779 - 792	778 - 791
48	24	6	SER	SER	ILE	ILE	1	B	B	779 - 792	778 - 791
49	25	6	LYS	LYS	LYS	LYS	2	A	A	793	792
50	25	6	LYS	LYS	LYS	LYS	2	B	B	793	792
51	26	6	ALA	ALA	GLU	GLU	1	A	A	794 - 801	793 - 800
52	26	6	ALA	ALA	GLU	GLU	1	B	B	794 - 801	793 - 800
53	27	6	ARG	ARG	ARG	ARG	2	A	A	802	801
54	27	6	ARG	ARG	ARG	ARG	2	B	B	802	801
55	28	6	ILE	ILE	GLU	GLU	1	A	A	803 - 817	802 - 816
56	28	6	ILE	ILE	GLU	GLU	1	B	B	803 - 817	802 - 816
57	29	6	TYR	TYR	ASP	ASP	2	A	A	818 - 825	817 - 824
58	29	6	TYR	TYR	ASP	ASP	2	B	B	818 - 825	817 - 824
59	30	6	ALA	ALA	GLY	GLY	1	A	A	826 - 828	825 - 827
60	30	6	ALA	ALA	GLY	GLY	1	B	B	826 - 828	825 - 827
61	31	6	LEU	LEU	GLN	GLN	2	A	A	829 - 832	828 - 831
62	31	6	LEU	LEU	GLN	GLN	2	B	B	829 - 832	828 - 831
63	32	6	GLU	GLU	ILE	ILE	1	A	A	833 - 837	832 - 836
64	32	6	GLU	GLU	ILE	ILE	1	B	B	833 - 837	832 - 836
65	33	6	ILE	ILE	GLN	GLN	2	A	A	838 - 846	837 - 845
66	33	6	ILE	ILE	GLN	GLN	2	B	B	838 - 846	837 - 845
67	34	6	MET	MET	VAL	VAL	1	A	A	847 - 849	846 - 848
68	34	6	MET	MET	VAL	VAL	1	B	B	847 - 849	846 - 848
69	35	6	GLN	GLN	LYS	LYS	2	A	A	850 - 852	849 - 851
70	35	6	GLN	GLN	LYS	LYS	2	B	B	850 - 852	849 - 851
71	36	6	LEU	LEU	GLY	GLY	1	A	A	853 - 856	852 - 855
72	36	6	LEU	LEU	GLY	GLY	1	B	B	853 - 856	852 - 855
73	37	6	LYS	LYS	LYS	LYS	2	A	A	857	856
74	37	6	LYS	LYS	LYS	LYS	2	B	B	857	856
75	38	6	THR	THR	MET	MET	1	A	A	858 - 863	857 - 862
76	38	6	THR	THR	MET	MET	1	B	B	858 - 863	857 - 862
77	39	6	ARG	ARG	LEU	LEU	2	A	A	864 - 875	863 - 874
78	39	6	ARG	ARG	LEU	LEU	2	B	B	864 - 875	863 - 874
79	40	6	ASN	ASN	ARG	ARG	1	A	A	876 - 885	875 - 884
80	40	6	ASN	ASN	ARG	ARG	1	B	B	876 - 885	875 - 884

NCS ensembles :

ID
1
2
3
4
5
6

Components

Protein , 1 types, 2 molecules A B

#1: Protein

A B Iron-responsive element binding protein 1 / IRE-BP 1 / Iron regulatory protein 1 / IRP1 / Ferritin repressor protein / Aconitate hydratase / Citrate hydro-lyase / Aconitase

Details:

Mass: 98374.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): K38/pGP1-2 / References: UniProt: P21399, aconitate hydratase

Non-polymers , 5 types, 978 molecules

#2: Chemical

A-890 B-890 B-891 ChemComp-ACT / ACETATE ION

Details:

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

#3: Chemical

A-1000 B-1000 ChemComp-SF4 / IRON/SULFUR CLUSTER

Details:

Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄

#4: Chemical

A-1001 A-1002 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃

#5: Chemical

B-1001 ChemComp-FMT / FORMIC ACID

Details:

Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 970 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.13 ų/Da / Density % sol: 42.23 %
• Crystal grow: Temperature: 293 K / pH: 8.1 / Details: pH 8.1, temperature 293K

Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
2,1		1

Diffraction source

Source	Site	Beamline	ID	Wavelength
SYNCHROTRON	ESRF	ID14-4	1	0.939
SYNCHROTRON	ESRF	BM30A	2	1.741417

Detector

ID	Date
1	Apr 5, 2003
2	Sep 4, 2003

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
2	SINGLE WAVELENGTH	M	x-ray	1
1	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.939	1
2	1.741417	1

• Reflection: Resolution: 1.85→29.5 Å / Num. obs: 138110 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2 % / R_merge(I) obs: 0.063 / Net I/σ(I): 8.6
• Reflection shell: Resolution: 1.85→2 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.262 / Mean I/σ(I) obs: 3 / % possible all: 92.1

Processing

Software

Name	Version	Classification	NB
REFMAC	5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3X

2b3x

Resolution: 1.85→29.5 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.896 / SU B: 9.904 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE SUBSTRATE (CITRATE/ISOCITRATE/CIS_ACONITATE) DENSITY IS NOT WELL DEFINED AND IT MAY REPRESENT A MIXTURE OF PARTIALLY BOUND CONFORMERS, INCLUDING A SUBSTRATE-FREE STATE. THIS ENTRY CONTAINS THE RESULTS OF AN ATTEMPT TO MODEL SUBSTRATE WITH ACETATE (ACT) AND FORMATE (FMT) FRAGMENTS. BECAUSE OF THE CRYSTAL HETEROGENEITY AND THE ABSENCE OF SPECIAL RESTRAINTS FOR SUBSTRATE/WATER BINDING, REFINED METAL-LIGAND DISTANCES SHOULD NOT BE TAKEN AS ACCURATE.

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.261	6949	5 %	RANDOM
Rwork	0.211	-	-	-
obs	0.213	131161	94 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 27.94 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.96 Å2	0 Å2	0.2 Å2
2-	-	2.36 Å2	0 Å2
3-	-	-	-1.53 Å2

Refinement step

Cycle: LAST / Resolution: 1.85→29.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13856	0	43	970	14869

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	14233
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.293	1.969	19330
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.89	5	1774
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.225	24.319	639
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.068	15	2363
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.811	15	82
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	2148
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	10868
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.3	7341
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.312	0.2	9823
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.198	0.5	1127
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.337	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.225	0.3	88
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.222	0.5	30
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	1.485	1.5	9078
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.986	2	14337
X-RAY DIFFRACTION	r_scbond_it	3.168	3	5764
X-RAY DIFFRACTION	r_scangle_it	4.108	4.5	4969
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	497	tight positional	0.04	0.07
2	1157	tight positional	0.05	0.07
3	905	tight positional	0.05	0.07
4	1204	tight positional	0.04	0.07
5	272	tight positional	0.05	0.07
6	1447	tight positional	0.05	0.07
1	100	medium positional	0.39	0.5
2	144	medium positional	0.46	0.5
3	85	medium positional	0.5	0.5
4	425	medium positional	0.59	0.5
5	222	medium positional	0.49	0.5
6	355	medium positional	0.45	0.5
1	6	loose positional	0.31	5
4	38	loose positional	1.51	5
5	31	loose positional	0.65	5
1	497	tight thermal	0.97	3
2	1157	tight thermal	0.95	3
3	905	tight thermal	0.97	3
4	1204	tight thermal	0.98	3
5	272	tight thermal	0.88	3
6	1447	tight thermal	0.94	3
1	100	medium thermal	1.64	4
2	144	medium thermal	1.49	4
3	85	medium thermal	1.4	4
4	425	medium thermal	1.52	4
5	222	medium thermal	1.28	4
6	355	medium thermal	1.67	4
1	6	loose thermal	1.07	10
4	38	loose thermal	3.18	10
5	31	loose thermal	1.38	10

LS refinement shell

Resolution: 1.85→1.93 Å / Total num. of bins used: 12

	Rfactor	Num. reflection	% reflection
Rfree	0.311	799	-
Rwork	0.237	15191	-
obs	-	-	94.16 %

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	1.5638	-0.6863	-0.2871	1.0852	0.5231	1.217	0.0466	-0.3981	-0.3011	0.0297	0.0359	0.2039	0.0821	-0.2403	-0.0824	-0.1638	-0.0207	-0.0097	0.0652	0.1422	-0.0016	3.475	10.254	14.005
2	0.404	0.033	0.4555	0.2794	-0.1332	1.0686	0.0925	-0.0737	-0.1217	0.0264	-0.0064	-0.0567	0.0603	-0.109	-0.0861	-0.1071	0.0058	0.0003	-0.1139	0.0457	-0.0317	31.108	14.358	14.529
3	1.8739	0.1084	0.0965	1.0182	-0.4364	0.5871	0.0173	0.0874	0.0724	-0.0915	0.0644	0.0704	0.0028	-0.1668	-0.0818	-0.1102	0.0211	0.0094	-0.0852	0.055	-0.0775	14.158	22.246	-2.198
4	0.7403	-0.0306	0.2822	1.3991	-0.5215	0.7984	-0.0299	0.1539	0.1709	-0.0161	-0.0547	-0.1417	-0.1583	0.0908	0.0846	-0.0852	-0.0025	0.0445	-0.1299	0.1022	0.0357	39.454	36.575	-7.063
5	0.8104	0.0825	0.2327	0.636	-0.0845	2.854	0.0914	0.0663	-0.1377	0.0232	-0.1448	-0.0844	0.238	0.0307	0.0534	-0.1408	0.0457	0.0182	-0.1868	0.0155	-0.005	37.537	12.813	9.895
6	1.1336	-0.1923	0.2328	0.8487	0.205	0.886	0.0305	-0.0173	0.2121	0.0841	-0.0304	-0.0381	-0.1668	-0.1828	-0.0001	-0.0412	0.048	0.053	-0.1295	0.0362	-0.0171	29.04	35.96	28.467
7	0.9936	0.5222	-0.0595	2.3857	-0.7686	1.5334	-0.0476	-0.1442	0.1408	0.2183	-0.094	0.0412	-0.193	0.0298	0.1417	-0.0668	0.03	-0.0284	-0.0408	0.013	-0.108	47.168	-10.838	45.878
8	0.6808	-0.009	0.4339	0.283	0.1702	0.8597	-0.1283	0.054	0.1228	-0.0601	-0.0664	0.0554	-0.1542	0.1795	0.1947	-0.0623	0.0028	-0.0261	-0.0797	0.0512	-0.0618	38.123	-14.931	19.712
9	0.645	-0.3549	0.4914	1.0445	0.4231	1.4859	-0.0244	0.0367	0.0636	0.0422	0.0737	-0.0519	0.1153	0.3213	-0.0494	-0.1158	0.0389	0.007	0.0164	0.0605	-0.0812	59.169	-22.954	30.541
10	0.9491	-0.6118	1.1185	1.0165	-1.0429	2.203	0.3504	0.2883	-0.1857	-0.3382	-0.0886	0.0027	0.8045	0.3971	-0.2619	0.2298	0.1718	-0.0643	0.0998	-0.024	-0.0829	55.675	-37.251	5.145
11	2.8676	0.3661	-0.5371	0.7018	0.0179	1.0325	-0.0108	-0.0017	0.2112	-0.0619	-0.1828	0.0401	-0.2012	0.238	0.1937	-0.0549	-0.0123	-0.0389	-0.0668	0.1156	-0.1064	40.411	-13.38	11.984
12	0.7461	0.024	0.671	0.8398	-0.2223	1.5555	0.1109	-0.0778	-0.0469	-0.0097	-0.0982	0.0705	0.3942	-0.0341	-0.0126	0.0171	0.0111	0.0299	-0.1865	0.0116	-0.0685	25.618	-36.448	25.929

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 74
2	X-RAY DIFFRACTION	1	A	1003 - 1028
3	X-RAY DIFFRACTION	2	A	75 - 240
4	X-RAY DIFFRACTION	2	A	1034 - 1111
5	X-RAY DIFFRACTION	3	A	241 - 367
6	X-RAY DIFFRACTION	4	A	368 - 590
7	X-RAY DIFFRACTION	4	A	1182 - 1265
8	X-RAY DIFFRACTION	5	A	591 - 653
9	X-RAY DIFFRACTION	5	A	1279 - 1309
10	X-RAY DIFFRACTION	6	A	654 - 889
11	X-RAY DIFFRACTION	7	B	2 - 74
12	X-RAY DIFFRACTION	7	B	1004 - 1029
13	X-RAY DIFFRACTION	8	B	75 - 240
14	X-RAY DIFFRACTION	9	B	241 - 367
15	X-RAY DIFFRACTION	9	B	1108 - 1158
16	X-RAY DIFFRACTION	10	B	368 - 590
17	X-RAY DIFFRACTION	10	B	1167 - 1212
18	X-RAY DIFFRACTION	11	B	591 - 653
19	X-RAY DIFFRACTION	11	B	1222 - 1250
20	X-RAY DIFFRACTION	12	B	654 - 889