PDB-2nox: Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia me...

ID or keywords:

Entry

Database: PDB / ID: 2nox

Title

Crystal structure of tryptophan 2,3-dioxygenase from Ralstonia metallidurans

Components

Tryptophan 2,3-dioxygenase

Keywords

OXIDOREDUCTASE / helical bundle / heme protein

Function / homology

Function and homology information

L-tryptophan catabolic process to acetyl-CoA / tryptophan 2,3-dioxygenase / L-tryptophan 2,3-dioxygenase activity / L-tryptophan catabolic process to kynurenine / quinolinate biosynthetic process / NAD+ biosynthetic process / catalytic complex / heme binding / metal ion binding / identical protein binding
Similarity search - Function

Biological species

Cupriavidus metallidurans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Zhang, Y. / Kang, S.A. / Mukherjee, T. / Bale, S. / Crane, B.R. / Begley, T.P. / Ealick, S.E.

Citation

Journal: Biochemistry / Year: 2007
Title: Crystal structure and mechanism of tryptophan 2,3-dioxygenase, a heme enzyme involved in tryptophan catabolism and in quinolinate biosynthesis.
Authors: Zhang, Y. / Kang, S.A. / Mukherjee, T. / Bale, S. / Crane, B.R. / Begley, T.P. / Ealick, S.E.

History

Deposition	Oct 26, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nox.cif.gz	874.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2nox.ent.gz	731.4 KB	Display	PDB format
PDBx/mmJSON format	2nox.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2nox_validation.pdf.gz	5.7 MB	Display	wwPDB validaton report
Full document	2nox_full_validation.pdf.gz	5.8 MB	Display
Data in XML	2nox_validation.xml.gz	173.7 KB	Display
Data in CIF	2nox_validation.cif.gz	230.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/no/2nox ftp://data.pdbj.org/pub/pdb/validation_reports/no/2nox	HTTPS FTP

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Related structure data

Related structure data	1yw0S S: Starting model for refinement
Similar structure data	3bk9-1 2nw7-d 3e08-1 3k9w-1 1u0f-d 1iat-1 6v26-2 2o2d-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1yw0S

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tryptophan 2,3-dioxygenase

B: Tryptophan 2,3-dioxygenase

C: Tryptophan 2,3-dioxygenase

D: Tryptophan 2,3-dioxygenase

E: Tryptophan 2,3-dioxygenase

F: Tryptophan 2,3-dioxygenase

G: Tryptophan 2,3-dioxygenase

H: Tryptophan 2,3-dioxygenase

I: Tryptophan 2,3-dioxygenase

J: Tryptophan 2,3-dioxygenase

K: Tryptophan 2,3-dioxygenase

L: Tryptophan 2,3-dioxygenase

M: Tryptophan 2,3-dioxygenase

N: Tryptophan 2,3-dioxygenase

O: Tryptophan 2,3-dioxygenase

P: Tryptophan 2,3-dioxygenase

hetero molecules

531 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tryptophan 2,3-dioxygenase

B: Tryptophan 2,3-dioxygenase

C: Tryptophan 2,3-dioxygenase

D: Tryptophan 2,3-dioxygenase

hetero molecules

defined by author&software
133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Tryptophan 2,3-dioxygenase

F: Tryptophan 2,3-dioxygenase

G: Tryptophan 2,3-dioxygenase

H: Tryptophan 2,3-dioxygenase

hetero molecules

defined by author&software
133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: Tryptophan 2,3-dioxygenase

J: Tryptophan 2,3-dioxygenase

K: Tryptophan 2,3-dioxygenase

L: Tryptophan 2,3-dioxygenase

hetero molecules

defined by author&software
133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

M: Tryptophan 2,3-dioxygenase

N: Tryptophan 2,3-dioxygenase

O: Tryptophan 2,3-dioxygenase

P: Tryptophan 2,3-dioxygenase

hetero molecules

defined by author&software
133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.544, 132.121, 139.950
Angle α, β, γ (deg.)	66.970, 85.060, 89.890
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
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	TYR	TYR	LEU	LEU	2	A	A	43 - 53	25 - 35
2	1	1	TYR	TYR	LEU	LEU	2	B	B	43 - 53	25 - 35
3	1	1	TYR	TYR	LEU	LEU	2	C	C	43 - 53	25 - 35
4	1	1	TYR	TYR	LEU	LEU	2	D	D	43 - 53	25 - 35
5	1	1	TYR	TYR	LEU	LEU	2	E	E	43 - 53	25 - 35
6	1	1	TYR	TYR	LEU	LEU	2	F	F	43 - 53	25 - 35
7	1	1	TYR	TYR	LEU	LEU	2	G	G	43 - 53	25 - 35
8	1	1	TYR	TYR	LEU	LEU	2	H	H	43 - 53	25 - 35
9	1	1	TYR	TYR	LEU	LEU	2	I	I	43 - 53	25 - 35
10	1	1	TYR	TYR	LEU	LEU	2	J	J	43 - 53	25 - 35
11	1	1	TYR	TYR	LEU	LEU	2	K	K	43 - 53	25 - 35
12	1	1	TYR	TYR	LEU	LEU	2	L	L	43 - 53	25 - 35
13	1	1	TYR	TYR	LEU	LEU	2	M	M	43 - 53	25 - 35
14	1	1	TYR	TYR	LEU	LEU	2	N	N	43 - 53	25 - 35
15	1	1	TYR	TYR	LEU	LEU	2	O	O	43 - 53	25 - 35
16	1	1	TYR	TYR	LEU	LEU	2	P	P	43 - 53	25 - 35
17	2	1	GLU	GLU	LEU	LEU	2	A	A	65 - 137	47 - 119
18	2	1	GLU	GLU	LEU	LEU	2	B	B	65 - 137	47 - 119
19	2	1	GLU	GLU	LEU	LEU	2	C	C	65 - 137	47 - 119
20	2	1	GLU	GLU	LEU	LEU	2	D	D	65 - 137	47 - 119
21	2	1	GLU	GLU	LEU	LEU	2	E	E	65 - 137	47 - 119
22	2	1	GLU	GLU	LEU	LEU	2	F	F	65 - 137	47 - 119
23	2	1	GLU	GLU	LEU	LEU	2	G	G	65 - 137	47 - 119
24	2	1	GLU	GLU	LEU	LEU	2	H	H	65 - 137	47 - 119
25	2	1	GLU	GLU	LEU	LEU	2	I	I	65 - 137	47 - 119
26	2	1	GLU	GLU	LEU	LEU	2	J	J	65 - 137	47 - 119
27	2	1	GLU	GLU	LEU	LEU	2	K	K	65 - 137	47 - 119
28	2	1	GLU	GLU	LEU	LEU	2	L	L	65 - 137	47 - 119
29	2	1	GLU	GLU	LEU	LEU	2	M	M	65 - 137	47 - 119
30	2	1	GLU	GLU	LEU	LEU	2	N	N	65 - 137	47 - 119
31	2	1	GLU	GLU	LEU	LEU	2	O	O	65 - 137	47 - 119
32	2	1	GLU	GLU	LEU	LEU	2	P	P	65 - 137	47 - 119
33	3	1	TYR	TYR	GLU	GLU	2	A	A	146 - 206	128 - 188
34	3	1	TYR	TYR	GLU	GLU	2	B	B	146 - 206	128 - 188
35	3	1	TYR	TYR	GLU	GLU	2	C	C	146 - 206	128 - 188
36	3	1	TYR	TYR	GLU	GLU	2	D	D	146 - 206	128 - 188
37	3	1	TYR	TYR	GLU	GLU	2	E	E	146 - 206	128 - 188
38	3	1	TYR	TYR	GLU	GLU	2	F	F	146 - 206	128 - 188
39	3	1	TYR	TYR	GLU	GLU	2	G	G	146 - 206	128 - 188
40	3	1	TYR	TYR	GLU	GLU	2	H	H	146 - 206	128 - 188
41	3	1	TYR	TYR	GLU	GLU	2	I	I	146 - 206	128 - 188
42	3	1	TYR	TYR	GLU	GLU	2	J	J	146 - 206	128 - 188
43	3	1	TYR	TYR	GLU	GLU	2	K	K	146 - 206	128 - 188
44	3	1	TYR	TYR	GLU	GLU	2	L	L	146 - 206	128 - 188
45	3	1	TYR	TYR	GLU	GLU	2	M	M	146 - 206	128 - 188
46	3	1	TYR	TYR	GLU	GLU	2	N	N	146 - 206	128 - 188
47	3	1	TYR	TYR	GLU	GLU	2	O	O	146 - 206	128 - 188
48	3	1	TYR	TYR	GLU	GLU	2	P	P	146 - 206	128 - 188
49	4	1	ALA	ALA	ILE	ILE	2	A	A	217 - 265	199 - 247
50	4	1	ALA	ALA	ILE	ILE	2	B	B	217 - 265	199 - 247
51	4	1	ALA	ALA	ILE	ILE	2	C	C	217 - 265	199 - 247
52	4	1	ALA	ALA	ILE	ILE	2	D	D	217 - 265	199 - 247
53	4	1	ALA	ALA	ILE	ILE	2	E	E	217 - 265	199 - 247
54	4	1	ALA	ALA	ILE	ILE	2	F	F	217 - 265	199 - 247
55	4	1	ALA	ALA	ILE	ILE	2	G	G	217 - 265	199 - 247
56	4	1	ALA	ALA	ILE	ILE	2	H	H	217 - 265	199 - 247
57	4	1	ALA	ALA	ILE	ILE	2	I	I	217 - 265	199 - 247
58	4	1	ALA	ALA	ILE	ILE	2	J	J	217 - 265	199 - 247
59	4	1	ALA	ALA	ILE	ILE	2	K	K	217 - 265	199 - 247
60	4	1	ALA	ALA	ILE	ILE	2	L	L	217 - 265	199 - 247
61	4	1	ALA	ALA	ILE	ILE	2	M	M	217 - 265	199 - 247
62	4	1	ALA	ALA	ILE	ILE	2	N	N	217 - 265	199 - 247
63	4	1	ALA	ALA	ILE	ILE	2	O	O	217 - 265	199 - 247
64	4	1	ALA	ALA	ILE	ILE	2	P	P	217 - 265	199 - 247
65	5	1	VAL	VAL	LEU	LEU	2	A	A	277 - 284	259 - 266
66	5	1	VAL	VAL	LEU	LEU	2	B	B	277 - 284	259 - 266
67	5	1	VAL	VAL	LEU	LEU	2	C	C	277 - 284	259 - 266
68	5	1	VAL	VAL	LEU	LEU	2	D	D	277 - 284	259 - 266
69	5	1	VAL	VAL	LEU	LEU	2	E	E	277 - 284	259 - 266
70	5	1	VAL	VAL	LEU	LEU	2	F	F	277 - 284	259 - 266
71	5	1	VAL	VAL	LEU	LEU	2	G	G	277 - 284	259 - 266
72	5	1	VAL	VAL	LEU	LEU	2	H	H	277 - 284	259 - 266
73	5	1	VAL	VAL	LEU	LEU	2	I	I	277 - 284	259 - 266
74	5	1	VAL	VAL	LEU	LEU	2	J	J	277 - 284	259 - 266
75	5	1	VAL	VAL	LEU	LEU	2	K	K	277 - 284	259 - 266
76	5	1	VAL	VAL	LEU	LEU	2	L	L	277 - 284	259 - 266
77	5	1	VAL	VAL	LEU	LEU	2	M	M	277 - 284	259 - 266
78	5	1	VAL	VAL	LEU	LEU	2	N	N	277 - 284	259 - 266
79	5	1	VAL	VAL	LEU	LEU	2	O	O	277 - 284	259 - 266
80	5	1	VAL	VAL	LEU	LEU	2	P	P	277 - 284	259 - 266
81	6	1	PRO	PRO	LEU	LEU	2	A	A	290 - 299	272 - 281
82	6	1	PRO	PRO	LEU	LEU	2	B	B	290 - 299	272 - 281
83	6	1	PRO	PRO	LEU	LEU	2	C	C	290 - 299	272 - 281
84	6	1	PRO	PRO	LEU	LEU	2	D	D	290 - 299	272 - 281
85	6	1	PRO	PRO	LEU	LEU	2	E	E	290 - 299	272 - 281
86	6	1	PRO	PRO	LEU	LEU	2	F	F	290 - 299	272 - 281
87	6	1	PRO	PRO	LEU	LEU	2	G	G	290 - 299	272 - 281
88	6	1	PRO	PRO	LEU	LEU	2	H	H	290 - 299	272 - 281
89	6	1	PRO	PRO	LEU	LEU	2	I	I	290 - 299	272 - 281
90	6	1	PRO	PRO	LEU	LEU	2	J	J	290 - 299	272 - 281
91	6	1	PRO	PRO	LEU	LEU	2	K	K	290 - 299	272 - 281
92	6	1	PRO	PRO	LEU	LEU	2	L	L	290 - 299	272 - 281
93	6	1	PRO	PRO	LEU	LEU	2	M	M	290 - 299	272 - 281
94	6	1	PRO	PRO	LEU	LEU	2	N	N	290 - 299	272 - 281
95	6	1	PRO	PRO	LEU	LEU	2	O	O	290 - 299	272 - 281
96	6	1	PRO	PRO	LEU	LEU	2	P	P	290 - 299	272 - 281
97	7	1	SER	SER	ASN	ASN	5	A	A	54 - 64	36 - 46
98	7	1	SER	SER	ASN	ASN	5	B	B	54 - 64	36 - 46
99	7	1	SER	SER	ASN	ASN	5	C	C	54 - 64	36 - 46
100	7	1	SER	SER	ASN	ASN	5	D	D	54 - 64	36 - 46
101	7	1	SER	SER	ASN	ASN	5	E	E	54 - 64	36 - 46
102	7	1	SER	SER	ASN	ASN	5	F	F	54 - 64	36 - 46
103	7	1	SER	SER	ASN	ASN	5	G	G	54 - 64	36 - 46
104	7	1	SER	SER	ASN	ASN	5	H	H	54 - 64	36 - 46
105	7	1	SER	SER	ASN	ASN	5	I	I	54 - 64	36 - 46
106	7	1	SER	SER	ASN	ASN	5	J	J	54 - 64	36 - 46
107	7	1	SER	SER	ASN	ASN	5	K	K	54 - 64	36 - 46
108	7	1	SER	SER	ASN	ASN	5	L	L	54 - 64	36 - 46
109	7	1	SER	SER	ASN	ASN	5	M	M	54 - 64	36 - 46
110	7	1	SER	SER	ASN	ASN	5	N	N	54 - 64	36 - 46
111	7	1	SER	SER	ASN	ASN	5	O	O	54 - 64	36 - 46
112	7	1	SER	SER	ASN	ASN	5	P	P	54 - 64	36 - 46
113	8	1	GLY	GLY	SER	SER	5	A	A	138 - 145	120 - 127
114	8	1	GLY	GLY	SER	SER	5	B	B	138 - 145	120 - 127
115	8	1	GLY	GLY	SER	SER	5	C	C	138 - 145	120 - 127
116	8	1	GLY	GLY	SER	SER	5	D	D	138 - 145	120 - 127
117	8	1	GLY	GLY	SER	SER	5	E	E	138 - 145	120 - 127
118	8	1	GLY	GLY	SER	SER	5	F	F	138 - 145	120 - 127
119	8	1	GLY	GLY	SER	SER	5	G	G	138 - 145	120 - 127
120	8	1	GLY	GLY	SER	SER	5	H	H	138 - 145	120 - 127
121	8	1	GLY	GLY	SER	SER	5	I	I	138 - 145	120 - 127
122	8	1	GLY	GLY	SER	SER	5	J	J	138 - 145	120 - 127
123	8	1	GLY	GLY	SER	SER	5	K	K	138 - 145	120 - 127
124	8	1	GLY	GLY	SER	SER	5	L	L	138 - 145	120 - 127
125	8	1	GLY	GLY	SER	SER	5	M	M	138 - 145	120 - 127
126	8	1	GLY	GLY	SER	SER	5	N	N	138 - 145	120 - 127
127	8	1	GLY	GLY	SER	SER	5	O	O	138 - 145	120 - 127
128	8	1	GLY	GLY	SER	SER	5	P	P	138 - 145	120 - 127
129	9	1	ARG	ARG	ASN	ASN	5	A	A	207 - 216	189 - 198
130	9	1	ARG	ARG	ASN	ASN	5	B	B	207 - 216	189 - 198
131	9	1	ARG	ARG	ASN	ASN	5	C	C	207 - 216	189 - 198
132	9	1	ARG	ARG	ASN	ASN	5	D	D	207 - 216	189 - 198
133	9	1	ARG	ARG	ASN	ASN	5	E	E	207 - 216	189 - 198
134	9	1	ARG	ARG	ASN	ASN	5	F	F	207 - 216	189 - 198
135	9	1	ARG	ARG	ASN	ASN	5	G	G	207 - 216	189 - 198
136	9	1	ARG	ARG	ASN	ASN	5	H	H	207 - 216	189 - 198
137	9	1	ARG	ARG	ASN	ASN	5	I	I	207 - 216	189 - 198
138	9	1	ARG	ARG	ASN	ASN	5	J	J	207 - 216	189 - 198
139	9	1	ARG	ARG	ASN	ASN	5	K	K	207 - 216	189 - 198
140	9	1	ARG	ARG	ASN	ASN	5	L	L	207 - 216	189 - 198
141	9	1	ARG	ARG	ASN	ASN	5	M	M	207 - 216	189 - 198
142	9	1	ARG	ARG	ASN	ASN	5	N	N	207 - 216	189 - 198
143	9	1	ARG	ARG	ASN	ASN	5	O	O	207 - 216	189 - 198
144	9	1	ARG	ARG	ASN	ASN	5	P	P	207 - 216	189 - 198
145	10	1	ASP	ASP	PHE	PHE	5	A	A	285 - 289	267 - 271
146	10	1	ASP	ASP	PHE	PHE	5	B	B	285 - 289	267 - 271
147	10	1	ASP	ASP	PHE	PHE	5	C	C	285 - 289	267 - 271
148	10	1	ASP	ASP	PHE	PHE	5	D	D	285 - 289	267 - 271
149	10	1	ASP	ASP	PHE	PHE	5	E	E	285 - 289	267 - 271
150	10	1	ASP	ASP	PHE	PHE	5	F	F	285 - 289	267 - 271
151	10	1	ASP	ASP	PHE	PHE	5	G	G	285 - 289	267 - 271
152	10	1	ASP	ASP	PHE	PHE	5	H	H	285 - 289	267 - 271
153	10	1	ASP	ASP	PHE	PHE	5	I	I	285 - 289	267 - 271
154	10	1	ASP	ASP	PHE	PHE	5	J	J	285 - 289	267 - 271
155	10	1	ASP	ASP	PHE	PHE	5	K	K	285 - 289	267 - 271
156	10	1	ASP	ASP	PHE	PHE	5	L	L	285 - 289	267 - 271
157	10	1	ASP	ASP	PHE	PHE	5	M	M	285 - 289	267 - 271
158	10	1	ASP	ASP	PHE	PHE	5	N	N	285 - 289	267 - 271
159	10	1	ASP	ASP	PHE	PHE	5	O	O	285 - 289	267 - 271
160	10	1	ASP	ASP	PHE	PHE	5	P	P	285 - 289	267 - 271
1	1	2	GLY	GLY	GLY	GLY	2	A	A	266 - 276	248 - 258
2	1	2	GLY	GLY	GLY	GLY	2	I	I	266 - 276	248 - 258

NCS ensembles :

ID
1
2

Details

The biological unit is a tetramer. The unit cell (P1) contains four tetramers.

#1: Protein	Tryptophan 2,3-dioxygenase Mass: 32542.783 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Cupriavidus metallidurans (bacteria) / References: UniProt: Q1LK00, tryptophan 2,3-dioxygenase
#2: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1543 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.87 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.0 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
Detector	Date: Jan 1, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.21→50 Å / Num. all: 224640 / Num. obs: 224640 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / R_merge(I) obs: 0.074 / R_sym value: 0.074 / Χ²: 1.655 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.21→2.29 Å / Redundancy: 2 % / R_merge(I) obs: 0.974 / Num. unique all: 18873 / Χ²: 1.533 / % possible all: 80.5

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.2.0019	refinement
PDB_EXTRACT	2	data extraction
ADSC	QUANTUM	data collection
HKL-2000		data reduction
CNS		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1YW0

1yw0

Resolution: 2.4→50.12 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.923 / SU B: 17.039 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.622 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27	8503	5 %	RANDOM
R_work	0.21	-	-	-
all	0.21	170159	-	-
obs	0.21	170159	93.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 45.446 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.62 Å²	-0.06 Å²	-1.34 Å²
2-	-	0.32 Å²	0.27 Å²
3-	-	-	-0.93 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→50.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	34146	0	688	1543	36377

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	35905
X-RAY DIFFRACTION	r_angle_refined_deg	1.487	2.006	48937
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.392	5	4124
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.57	22.967	1827
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.632	15	5985
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.406	15	337
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	5031
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	27924
X-RAY DIFFRACTION	r_nbd_refined	0.245	0.3	18615
X-RAY DIFFRACTION	r_nbtor_refined	0.324	0.5	24341
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.219	0.5	3459
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.296	0.3	186
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.246	0.5	15
X-RAY DIFFRACTION	r_mcbond_it	4.168	2	21162
X-RAY DIFFRACTION	r_mcangle_it	5.842	3	33437
X-RAY DIFFRACTION	r_scbond_it	6.338	2	16938
X-RAY DIFFRACTION	r_scangle_it	7.762	3	15466

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	831	TIGHT POSITIONAL	0.19	0.05
1	2	B	831	TIGHT POSITIONAL	0.12	0.05
1	3	C	831	TIGHT POSITIONAL	0.14	0.05
1	4	D	831	TIGHT POSITIONAL	0.14	0.05
1	5	E	831	TIGHT POSITIONAL	0.11	0.05
1	6	F	831	TIGHT POSITIONAL	0.12	0.05
1	7	G	831	TIGHT POSITIONAL	0.12	0.05
1	8	H	831	TIGHT POSITIONAL	0.13	0.05
1	9	I	831	TIGHT POSITIONAL	0.14	0.05
1	10	J	831	TIGHT POSITIONAL	0.11	0.05
1	11	K	831	TIGHT POSITIONAL	0.13	0.05
1	12	L	831	TIGHT POSITIONAL	0.11	0.05
1	13	M	831	TIGHT POSITIONAL	0.13	0.05
1	14	N	831	TIGHT POSITIONAL	0.12	0.05
1	15	O	831	TIGHT POSITIONAL	0.12	0.05
1	16	P	831	TIGHT POSITIONAL	0.13	0.05
1	1	A	1038	MEDIUM POSITIONAL	0.56	0.5
1	2	B	1038	MEDIUM POSITIONAL	0.48	0.5
1	3	C	1038	MEDIUM POSITIONAL	0.65	0.5
1	4	D	1038	MEDIUM POSITIONAL	0.41	0.5
1	5	E	1038	MEDIUM POSITIONAL	0.41	0.5
1	6	F	1038	MEDIUM POSITIONAL	0.46	0.5
1	7	G	1038	MEDIUM POSITIONAL	0.47	0.5
1	8	H	1038	MEDIUM POSITIONAL	0.47	0.5
1	9	I	1038	MEDIUM POSITIONAL	0.49	0.5
1	10	J	1038	MEDIUM POSITIONAL	0.42	0.5
1	11	K	1038	MEDIUM POSITIONAL	0.55	0.5
1	12	L	1038	MEDIUM POSITIONAL	0.45	0.5
1	13	M	1038	MEDIUM POSITIONAL	0.47	0.5
1	14	N	1038	MEDIUM POSITIONAL	0.48	0.5
1	15	O	1038	MEDIUM POSITIONAL	0.56	0.5
1	16	P	1038	MEDIUM POSITIONAL	0.47	0.5
1	1	A	130	LOOSE POSITIONAL	0.64	5
1	2	B	130	LOOSE POSITIONAL	0.55	5
1	3	C	130	LOOSE POSITIONAL	0.62	5
1	4	D	130	LOOSE POSITIONAL	0.45	5
1	5	E	130	LOOSE POSITIONAL	0.44	5
1	6	F	130	LOOSE POSITIONAL	0.42	5
1	7	G	130	LOOSE POSITIONAL	0.57	5
1	8	H	130	LOOSE POSITIONAL	0.57	5
1	9	I	130	LOOSE POSITIONAL	0.59	5
1	10	J	130	LOOSE POSITIONAL	0.55	5
1	11	K	130	LOOSE POSITIONAL	0.56	5
1	12	L	130	LOOSE POSITIONAL	0.53	5
1	13	M	130	LOOSE POSITIONAL	0.41	5
1	14	N	130	LOOSE POSITIONAL	0.73	5
1	15	O	130	LOOSE POSITIONAL	0.55	5
1	16	P	130	LOOSE POSITIONAL	0.51	5
1	1	A	831	TIGHT THERMAL	0.66	0.5
1	2	B	831	TIGHT THERMAL	0.55	0.5
1	3	C	831	TIGHT THERMAL	0.56	0.5
1	4	D	831	TIGHT THERMAL	0.77	0.5
1	5	E	831	TIGHT THERMAL	0.54	0.5
1	6	F	831	TIGHT THERMAL	0.54	0.5
1	7	G	831	TIGHT THERMAL	0.52	0.5
1	8	H	831	TIGHT THERMAL	0.54	0.5
1	9	I	831	TIGHT THERMAL	0.51	0.5
1	10	J	831	TIGHT THERMAL	0.42	0.5
1	11	K	831	TIGHT THERMAL	0.43	0.5
1	12	L	831	TIGHT THERMAL	0.51	0.5
1	13	M	831	TIGHT THERMAL	0.53	0.5
1	14	N	831	TIGHT THERMAL	0.44	0.5
1	15	O	831	TIGHT THERMAL	0.47	0.5
1	16	P	831	TIGHT THERMAL	0.56	0.5
1	1	A	1038	MEDIUM THERMAL	4.45	2
1	2	B	1038	MEDIUM THERMAL	3.69	2
1	3	C	1038	MEDIUM THERMAL	3.7	2
1	4	D	1038	MEDIUM THERMAL	4.96	2
1	5	E	1038	MEDIUM THERMAL	3.68	2
1	6	F	1038	MEDIUM THERMAL	3.54	2
1	7	G	1038	MEDIUM THERMAL	3.77	2
1	8	H	1038	MEDIUM THERMAL	4.3	2
1	9	I	1038	MEDIUM THERMAL	3.48	2
1	10	J	1038	MEDIUM THERMAL	2.92	2
1	11	K	1038	MEDIUM THERMAL	3.51	2
1	12	L	1038	MEDIUM THERMAL	3.69	2
1	13	M	1038	MEDIUM THERMAL	3.8	2
1	14	N	1038	MEDIUM THERMAL	3.16	2
1	15	O	1038	MEDIUM THERMAL	3.43	2
1	16	P	1038	MEDIUM THERMAL	3.76	2
1	1	A	130	LOOSE THERMAL	10.84	10
1	2	B	130	LOOSE THERMAL	8.46	10
1	3	C	130	LOOSE THERMAL	6.87	10
1	4	D	130	LOOSE THERMAL	12.32	10
1	5	E	130	LOOSE THERMAL	8.38	10
1	6	F	130	LOOSE THERMAL	8.89	10
1	7	G	130	LOOSE THERMAL	10.03	10
1	8	H	130	LOOSE THERMAL	9.26	10
1	9	I	130	LOOSE THERMAL	8.71	10
1	10	J	130	LOOSE THERMAL	6.36	10
1	11	K	130	LOOSE THERMAL	7.17	10
1	12	L	130	LOOSE THERMAL	8.97	10
1	13	M	130	LOOSE THERMAL	8.61	10
1	14	N	130	LOOSE THERMAL	7.63	10
1	15	O	130	LOOSE THERMAL	9.88	10
1	16	P	130	LOOSE THERMAL	8.23	10
2	1	A	44	TIGHT POSITIONAL	0.07	0.05
2	1	A	30	MEDIUM POSITIONAL	0.5	0.5
2	1	A	44	TIGHT THERMAL	0.75	0.5
2	1	A	30	MEDIUM THERMAL	3.53	2

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.361	581	-
R_work	0.244	10346	-
obs	-	10927	82 %

Refinement TLS params.

Method: refined / Origin x: 71.8281 Å / Origin y: 82.9725 Å / Origin z: 69.8378 Å

	11	12	13	21	22	23	31	32	33
T	-0.0149 Å²	0 Å²	-0.0239 Å²	-	-0.0482 Å²	-0.0013 Å²	-	-	-0.0632 Å²
L	0.1581 °²	-0.0001 °²	-0.0262 °²	-	0.1682 °²	0.0171 °²	-	-	0.0595 °²
S	0.0239 Å °	0.0369 Å °	-0.0033 Å °	-0.056 Å °	-0.0027 Å °	0.0288 Å °	0.0657 Å °	0.0205 Å °	-0.0212 Å °

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	A	A	39 - 299	21 - 281
2	B	B	30 - 299	12 - 281
3	C	C	40 - 299	22 - 281
4	D	D	41 - 299	23 - 281
5	E	E	39 - 299	21 - 281
6	F	F	35 - 299	17 - 281
7	G	G	40 - 299	22 - 281
8	H	H	41 - 299	23 - 281
9	I	I	41 - 299	23 - 281
10	J	J	39 - 299	21 - 281
11	K	K	39 - 299	21 - 281
12	L	L	40 - 299	22 - 281
13	M	M	40 - 299	22 - 281
14	N	N	40 - 299	22 - 281
15	O	O	39 - 299	21 - 281
16	P	P	41 - 299	23 - 281

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