PDB-2bys: CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA IN complex wi...

ID or keywords:

Entry

Database: PDB / ID: 2bys

Title

CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA IN complex with lobeline

Components

ACETYLCHOLINE-BINDING PROTEIN

Keywords

RECEPTOR / ACETYLCHOLINE BINDING PROTEIN / NICOTINIC ACETYLCHOLINE / CONFORMATIONAL FLEXIBILITY / LOBELINE

Function / homology

Function and homology information

extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
Similarity search - Function

Biological species

APLYSIA CALIFORNICA (California sea hare)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Hansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y.

Citation

Journal: Embo J. / Year: 2005
Title: Structures of Aplysia Achbp Complexes with Nicotinic Agonists and Antagonists Reveal Distinctive Binding Interfaces and Conformations.
Authors: Hansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y.

History

Deposition	Aug 4, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 5, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Apr 3, 2019	Group: Data collection / Other / Source and taxonomy Category: entity_src_gen / pdbx_database_proc / pdbx_database_status Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _pdbx_database_status.status_code_sf / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2bys.cif.gz	457 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2bys.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/by/2bys ftp://data.pdbj.org/pub/pdb/validation_reports/by/2bys	HTTPS FTP

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Related structure data

Related structure data	2bynSC 2bypC 2byqC 2byrC 2br7 2br8 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5oal-1 2xnu-d 5bw2-d 5ke4-d 4zk4-d 5ain-d 2y56-d 4xk9-1 5oal-3 2byr-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4) #71 - Nov 2005 Acetylcholine Receptor similarity (4)

Deposited unit

A: ACETYLCHOLINE-BINDING PROTEIN

B: ACETYLCHOLINE-BINDING PROTEIN

C: ACETYLCHOLINE-BINDING PROTEIN

D: ACETYLCHOLINE-BINDING PROTEIN

E: ACETYLCHOLINE-BINDING PROTEIN

F: ACETYLCHOLINE-BINDING PROTEIN

G: ACETYLCHOLINE-BINDING PROTEIN

H: ACETYLCHOLINE-BINDING PROTEIN

I: ACETYLCHOLINE-BINDING PROTEIN

J: ACETYLCHOLINE-BINDING PROTEIN

hetero molecules

262 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ACETYLCHOLINE-BINDING PROTEIN

B: ACETYLCHOLINE-BINDING PROTEIN

C: ACETYLCHOLINE-BINDING PROTEIN

D: ACETYLCHOLINE-BINDING PROTEIN

E: ACETYLCHOLINE-BINDING PROTEIN

hetero molecules

defined by author&software
131 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: ACETYLCHOLINE-BINDING PROTEIN

G: ACETYLCHOLINE-BINDING PROTEIN

H: ACETYLCHOLINE-BINDING PROTEIN

I: ACETYLCHOLINE-BINDING PROTEIN

J: ACETYLCHOLINE-BINDING PROTEIN

hetero molecules

defined by author&software
131 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.764, 85.731, 117.318
Angle α, β, γ (deg.)	89.95, 97.33, 106.64
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	E
4	1	F
5	1	H
6	1	J
1	2	B
2	2	G
1	3	D
2	3	I

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	GLN	GLN	PHE	PHE	5	A	A	3 - 14	11 - 22
2	1	1	GLN	GLN	PHE	PHE	5	C	C	3 - 14	11 - 22
3	1	1	GLN	GLN	PHE	PHE	5	E	E	3 - 14	11 - 22
4	1	1	GLN	GLN	PHE	PHE	5	F	F	3 - 14	11 - 22
5	1	1	GLN	GLN	PHE	PHE	5	H	H	3 - 14	11 - 22
6	1	1	GLN	GLN	PHE	PHE	5	J	J	3 - 14	11 - 22
1	2	1	GLY	GLY	THR	THR	2	A	A	22 - 24	30 - 32
2	2	1	GLY	GLY	THR	THR	2	C	C	22 - 24	30 - 32
3	2	1	GLY	GLY	THR	THR	2	E	E	22 - 24	30 - 32
4	2	1	GLY	GLY	THR	THR	2	F	F	22 - 24	30 - 32
5	2	1	GLY	GLY	THR	THR	2	H	H	22 - 24	30 - 32
6	2	1	GLY	GLY	THR	THR	2	J	J	22 - 24	30 - 32
1	3	1	ASP	ASP	LEU	LEU	2	A	A	26 - 37	34 - 45
2	3	1	ASP	ASP	LEU	LEU	2	C	C	26 - 37	34 - 45
3	3	1	ASP	ASP	LEU	LEU	2	E	E	26 - 37	34 - 45
4	3	1	ASP	ASP	LEU	LEU	2	F	F	26 - 37	34 - 45
5	3	1	ASP	ASP	LEU	LEU	2	H	H	26 - 37	34 - 45
6	3	1	ASP	ASP	LEU	LEU	2	J	J	26 - 37	34 - 45
1	4	1	ASP	ASP	TYR	TYR	2	A	A	39 - 54	47 - 62
2	4	1	ASP	ASP	TYR	TYR	2	C	C	39 - 54	47 - 62
3	4	1	ASP	ASP	TYR	TYR	2	E	E	39 - 54	47 - 62
4	4	1	ASP	ASP	TYR	TYR	2	F	F	39 - 54	47 - 62
5	4	1	ASP	ASP	TYR	TYR	2	H	H	39 - 54	47 - 62
6	4	1	ASP	ASP	TYR	TYR	2	J	J	39 - 54	47 - 62
1	5	1	GLU	GLU	GLN	GLN	5	A	A	56 - 58	64 - 66
2	5	1	GLU	GLU	GLN	GLN	5	C	C	56 - 58	64 - 66
3	5	1	GLU	GLU	GLN	GLN	5	E	E	56 - 58	64 - 66
4	5	1	GLU	GLU	GLN	GLN	5	F	F	56 - 58	64 - 66
5	5	1	GLU	GLU	GLN	GLN	5	H	H	56 - 58	64 - 66
6	5	1	GLU	GLU	GLN	GLN	5	J	J	56 - 58	64 - 66
1	6	1	TRP	TRP	ASP	ASP	3	A	A	60 - 68	68 - 76
2	6	1	TRP	TRP	ASP	ASP	3	C	C	60 - 68	68 - 76
3	6	1	TRP	TRP	ASP	ASP	3	E	E	60 - 68	68 - 76
4	6	1	TRP	TRP	ASP	ASP	3	F	F	60 - 68	68 - 76
5	6	1	TRP	TRP	ASP	ASP	3	H	H	60 - 68	68 - 76
6	6	1	TRP	TRP	ASP	ASP	3	J	J	60 - 68	68 - 76
1	7	1	PRO	PRO	ILE	ILE	5	A	A	69 - 85	77 - 93
2	7	1	PRO	PRO	ILE	ILE	5	C	C	69 - 85	77 - 93
3	7	1	PRO	PRO	ILE	ILE	5	E	E	69 - 85	77 - 93
4	7	1	PRO	PRO	ILE	ILE	5	F	F	69 - 85	77 - 93
5	7	1	PRO	PRO	ILE	ILE	5	H	H	69 - 85	77 - 93
6	7	1	PRO	PRO	ILE	ILE	5	J	J	69 - 85	77 - 93
1	8	1	TRP	TRP	ALA	ALA	2	A	A	86 - 92	94 - 100
2	8	1	TRP	TRP	ALA	ALA	2	C	C	86 - 92	94 - 100
3	8	1	TRP	TRP	ALA	ALA	2	E	E	86 - 92	94 - 100
4	8	1	TRP	TRP	ALA	ALA	2	F	F	86 - 92	94 - 100
5	8	1	TRP	TRP	ALA	ALA	2	H	H	86 - 92	94 - 100
6	8	1	TRP	TRP	ALA	ALA	2	J	J	86 - 92	94 - 100
1	9	1	PRO	PRO	PRO	PRO	2	A	A	98 - 104	106 - 112
2	9	1	PRO	PRO	PRO	PRO	2	C	C	98 - 104	106 - 112
3	9	1	PRO	PRO	PRO	PRO	2	E	E	98 - 104	106 - 112
4	9	1	PRO	PRO	PRO	PRO	2	F	F	98 - 104	106 - 112
5	9	1	PRO	PRO	PRO	PRO	2	H	H	98 - 104	106 - 112
6	9	1	PRO	PRO	PRO	PRO	2	J	J	98 - 104	106 - 112
1	10	1	ILE	ILE	ALA	ALA	2	A	A	106 - 120	114 - 128
2	10	1	ILE	ILE	ALA	ALA	2	C	C	106 - 120	114 - 128
3	10	1	ILE	ILE	ALA	ALA	2	E	E	106 - 120	114 - 128
4	10	1	ILE	ILE	ALA	ALA	2	F	F	106 - 120	114 - 128
5	10	1	ILE	ILE	ALA	ALA	2	H	H	106 - 120	114 - 128
6	10	1	ILE	ILE	ALA	ALA	2	J	J	106 - 120	114 - 128
1	11	1	LEU	LEU	MET	MET	2	A	A	123 - 126	131 - 134
2	11	1	LEU	LEU	MET	MET	2	C	C	123 - 126	131 - 134
3	11	1	LEU	LEU	MET	MET	2	E	E	123 - 126	131 - 134
4	11	1	LEU	LEU	MET	MET	2	F	F	123 - 126	131 - 134
5	11	1	LEU	LEU	MET	MET	2	H	H	123 - 126	131 - 134
6	11	1	LEU	LEU	MET	MET	2	J	J	123 - 126	131 - 134
1	12	1	CYS	CYS	CYS	CYS	5	A	A	127 - 140	135 - 148
2	12	1	CYS	CYS	CYS	CYS	5	C	C	127 - 140	135 - 148
3	12	1	CYS	CYS	CYS	CYS	5	E	E	127 - 140	135 - 148
4	12	1	CYS	CYS	CYS	CYS	5	F	F	127 - 140	135 - 148
5	12	1	CYS	CYS	CYS	CYS	5	H	H	127 - 140	135 - 148
6	12	1	CYS	CYS	CYS	CYS	5	J	J	127 - 140	135 - 148
1	13	1	ALA	ALA	SER	SER	2	A	A	141 - 150	149 - 158
2	13	1	ALA	ALA	SER	SER	2	C	C	141 - 150	149 - 158
3	13	1	ALA	ALA	SER	SER	2	E	E	141 - 150	149 - 158
4	13	1	ALA	ALA	SER	SER	2	F	F	141 - 150	149 - 158
5	13	1	ALA	ALA	SER	SER	2	H	H	141 - 150	149 - 158
6	13	1	ALA	ALA	SER	SER	2	J	J	141 - 150	149 - 158
1	14	1	GLY	GLY	THR	THR	5	A	A	151 - 160	159 - 168
2	14	1	GLY	GLY	THR	THR	5	C	C	151 - 160	159 - 168
3	14	1	GLY	GLY	THR	THR	5	E	E	151 - 160	159 - 168
4	14	1	GLY	GLY	THR	THR	5	F	F	151 - 160	159 - 168
5	14	1	GLY	GLY	THR	THR	5	H	H	151 - 160	159 - 168
6	14	1	GLY	GLY	THR	THR	5	J	J	151 - 160	159 - 168
1	15	1	VAL	VAL	SER	SER	2	A	A	163 - 166	171 - 174
2	15	1	VAL	VAL	SER	SER	2	C	C	163 - 166	171 - 174
3	15	1	VAL	VAL	SER	SER	2	E	E	163 - 166	171 - 174
4	15	1	VAL	VAL	SER	SER	2	F	F	163 - 166	171 - 174
5	15	1	VAL	VAL	SER	SER	2	H	H	163 - 166	171 - 174
6	15	1	VAL	VAL	SER	SER	2	J	J	163 - 166	171 - 174
1	16	1	TYR	TYR	VAL	VAL	2	A	A	168 - 185	176 - 193
2	16	1	TYR	TYR	VAL	VAL	2	C	C	168 - 185	176 - 193
3	16	1	TYR	TYR	VAL	VAL	2	E	E	168 - 185	176 - 193
4	16	1	TYR	TYR	VAL	VAL	2	F	F	168 - 185	176 - 193
5	16	1	TYR	TYR	VAL	VAL	2	H	H	168 - 185	176 - 193
6	16	1	TYR	TYR	VAL	VAL	2	J	J	168 - 185	176 - 193
1	17	1	VAL	VAL	ILE	ILE	5	A	A	185 - 196	193 - 204
2	17	1	VAL	VAL	ILE	ILE	5	C	C	185 - 196	193 - 204
3	17	1	VAL	VAL	ILE	ILE	5	E	E	185 - 196	193 - 204
4	17	1	VAL	VAL	ILE	ILE	5	F	F	185 - 196	193 - 204
5	17	1	VAL	VAL	ILE	ILE	5	H	H	185 - 196	193 - 204
6	17	1	VAL	VAL	ILE	ILE	5	J	J	185 - 196	193 - 204
1	18	1	ASP	ASP	VAL	VAL	2	A	A	197 - 202	205 - 210
2	18	1	ASP	ASP	VAL	VAL	2	C	C	197 - 202	205 - 210
3	18	1	ASP	ASP	VAL	VAL	2	E	E	197 - 202	205 - 210
4	18	1	ASP	ASP	VAL	VAL	2	F	F	197 - 202	205 - 210
5	18	1	ASP	ASP	VAL	VAL	2	H	H	197 - 202	205 - 210
6	18	1	ASP	ASP	VAL	VAL	2	J	J	197 - 202	205 - 210
1	19	1	LYS	LYS	GLU	GLU	5	A	A	203 - 206	211 - 214
2	19	1	LYS	LYS	GLU	GLU	5	C	C	203 - 206	211 - 214
3	19	1	LYS	LYS	GLU	GLU	5	E	E	203 - 206	211 - 214
4	19	1	LYS	LYS	GLU	GLU	5	F	F	203 - 206	211 - 214
5	19	1	LYS	LYS	GLU	GLU	5	H	H	203 - 206	211 - 214
6	19	1	LYS	LYS	GLU	GLU	5	J	J	203 - 206	211 - 214
1	1	2	GLN	GLN	PHE	PHE	5	B	B	3 - 14	11 - 22
2	1	2	GLN	GLN	PHE	PHE	5	G	G	3 - 14	11 - 22
1	2	2	TYR	TYR	PRO	PRO	5	B	B	20 - 28	28 - 36
2	2	2	TYR	TYR	PRO	PRO	5	G	G	20 - 28	28 - 36
1	3	2	LEU	LEU	VAL	VAL	1	B	B	29 - 41	37 - 49
2	3	2	LEU	LEU	VAL	VAL	1	G	G	29 - 41	37 - 49
1	4	2	ALA	ALA	GLN	GLN	1	B	B	43 - 58	51 - 66
2	4	2	ALA	ALA	GLN	GLN	1	G	G	43 - 58	51 - 66
1	5	2	TRP	TRP	ARG	ARG	4	B	B	60 - 79	68 - 87
2	5	2	TRP	TRP	ARG	ARG	4	G	G	60 - 79	68 - 87
1	6	2	THR	THR	THR	THR	1	B	B	80 - 96	88 - 104
2	6	2	THR	THR	THR	THR	1	G	G	80 - 96	88 - 104
1	7	2	VAL	VAL	PRO	PRO	1	B	B	101 - 104	109 - 112
2	7	2	VAL	VAL	PRO	PRO	1	G	G	101 - 104	109 - 112
1	8	2	ILE	ILE	GLN	GLN	5	B	B	106 - 121	114 - 129
2	8	2	ILE	ILE	GLN	GLN	5	G	G	106 - 121	114 - 129
1	9	2	ARG	ARG	PRO	PRO	1	B	B	122 - 129	130 - 137
2	9	2	ARG	ARG	PRO	PRO	1	G	G	122 - 129	130 - 137
1	10	2	THR	THR	GLU	GLU	5	B	B	130 - 136	138 - 144
2	10	2	THR	THR	GLU	GLU	5	G	G	130 - 136	138 - 144
1	11	2	GLY	GLY	SER	SER	1	B	B	137 - 150	145 - 158
2	11	2	GLY	GLY	SER	SER	1	G	G	137 - 150	145 - 158
1	12	2	ILE	ILE	THR	THR	2	B	B	154 - 160	162 - 168
2	12	2	ILE	ILE	THR	THR	2	G	G	154 - 160	162 - 168
1	13	2	VAL	VAL	ARG	ARG	1	B	B	163 - 183	171 - 191
2	13	2	VAL	VAL	ARG	ARG	1	G	G	163 - 183	171 - 191
1	14	2	GLN	GLN	GLU	GLU	3	B	B	184 - 193	192 - 201
2	14	2	GLN	GLN	GLU	GLU	3	G	G	184 - 193	192 - 201
1	15	2	PRO	PRO	GLU	GLU	1	B	B	194 - 206	202 - 214
2	15	2	PRO	PRO	GLU	GLU	1	G	G	194 - 206	202 - 214
1	1	3	SER	SER	PHE	PHE	5	D	D	2 - 14	10 - 22
2	1	3	SER	SER	PHE	PHE	5	I	I	2 - 14	10 - 22
1	2	3	TYR	TYR	PRO	PRO	5	D	D	20 - 28	28 - 36
2	2	3	TYR	TYR	PRO	PRO	5	I	I	20 - 28	28 - 36
1	3	3	LEU	LEU	VAL	VAL	1	D	D	29 - 41	37 - 49
2	3	3	LEU	LEU	VAL	VAL	1	I	I	29 - 41	37 - 49
1	4	3	ALA	ALA	GLU	GLU	1	D	D	43 - 56	51 - 64
2	4	3	ALA	ALA	GLU	GLU	1	I	I	43 - 56	51 - 64
1	5	3	TRP	TRP	THR	THR	2	D	D	60 - 76	68 - 84
2	5	3	TRP	TRP	THR	THR	2	I	I	60 - 76	68 - 84
1	6	3	PHE	PHE	THR	THR	2	D	D	78 - 96	86 - 104
2	6	3	PHE	PHE	THR	THR	2	I	I	78 - 96	86 - 104
1	7	3	VAL	VAL	PRO	PRO	1	D	D	101 - 104	109 - 112
2	7	3	VAL	VAL	PRO	PRO	1	I	I	101 - 104	109 - 112
1	8	3	ILE	ILE	ALA	ALA	1	D	D	106 - 120	114 - 128
2	8	3	ILE	ILE	ALA	ALA	1	I	I	106 - 120	114 - 128
1	9	3	ARG	ARG	PRO	PRO	1	D	D	122 - 129	130 - 137
2	9	3	ARG	ARG	PRO	PRO	1	I	I	122 - 129	130 - 137
1	10	3	THR	THR	GLU	GLU	5	D	D	130 - 136	138 - 144
2	10	3	THR	THR	GLU	GLU	5	I	I	130 - 136	138 - 144
1	11	3	GLY	GLY	GLY	GLY	2	D	D	137 - 151	145 - 159
2	11	3	GLY	GLY	GLY	GLY	2	I	I	137 - 151	145 - 159
1	12	3	PHE	PHE	GLN	GLN	5	D	D	152 - 162	160 - 170
2	12	3	PHE	PHE	GLN	GLN	5	I	I	152 - 162	160 - 170
1	13	3	VAL	VAL	VAL	VAL	2	D	D	163 - 185	171 - 193
2	13	3	VAL	VAL	VAL	VAL	2	I	I	163 - 185	171 - 193
1	14	3	CYS	CYS	VAL	VAL	2	D	D	190 - 202	198 - 210
2	14	3	CYS	CYS	VAL	VAL	2	I	I	190 - 202	198 - 210

NCS ensembles :

ID
1
2
3

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.83709, -0.54705, 0.00014), (-0.54705, 0.83708, 0.00339), (-0.00197, 0.00275, -0.99999)	-29.9879, 35.8926, 57.8114
2	given	(-0.83944, -0.54343, -0.0022), (-0.54343, 0.83945, -0.00124), (0.00252, 0.00015, -0.99999)	-29.9769, 35.8723, 57.8966
3	given	(-0.83882, -0.54439, 0.00077), (-0.54439, 0.83882, -0.00272), (0.00083, -0.00271, -0.99999)	-29.8933, 35.8601, 57.8832
4	given	(-0.8386, -0.54473, -0.00138), (-0.54473, 0.8386, 0.00232), (-0.0001, 0.0027, -0.99999)	-29.941, 35.7902, 57.951
5	given	(-0.83909, -0.54398, -0.00085), (-0.54398, 0.83909, -0.0025), (0.00208, -0.00163, -0.99999)	-30.0912, 35.8425, 57.9232

#1: Protein	ACETYLCHOLINE-BINDING PROTEIN Mass: 25852.744 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare) Cell: SENSORY CELL / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / Tissue (production host): KIDNEY / References: UniProt: Q8WSF8
#2: Chemical	ChemComp-LOB / LOBELINE / 2-{(2S,6R)-6-[(2R)-2-HYDROXY-2-PHENYLETHYL]-1-METHYLPIPERIDIN-2-YL}-1-PHENYLETHANONE Mass: 337.455 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂₂H₂₇NO₂ / Comment: alkaloid*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1559 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	THE FIRST 17 RESIDUES OF THE GENBANK ENTRY CORRESPOND TO THE SIGNAL PEPTIDE THE EXTRA N-TERMINAL ...THE FIRST 17 RESIDUES OF THE GENBANK ENTRY CORRESPOND TO THE SIGNAL PEPTIDE THE EXTRA N-TERMINAL RESIDUES PRESENT IN THE COORDINATES CORRESPOND TO A FLAG EPITOPE INTRODUCED BY CLONING

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56 %
Crystal grow	pH: 7.5 / Details: 25% PEG 4K, 0.1 M HEPES, PH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97623
Detector	Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97623 Å / Relative weight: 1
Reflection	Resolution: 2.05→58 Å / Num. obs: 168545 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 2 % / B_iso Wilson estimate: 25.6 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2.05→2.16 Å / Redundancy: 2 % / R_merge(I) obs: 0.26 / Mean I/σ(I) obs: 2.5 / % possible all: 95.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYN

2byn

Resolution: 2.05→47.73 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.914 / SU B: 15.738 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.258	5025	3 %	RANDOM
R_work	0.216	-	-	-
obs	0.217	161270	94.5 %	-

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: 32.39 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.24 Å²	2.24 Å²	0.25 Å²
2-	-	-1.31 Å²	0.3 Å²
3-	-	-	-2.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→47.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16324	0	250	1559	18133

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	17410
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15219
X-RAY DIFFRACTION	r_angle_refined_deg	1.162	1.963	23791
X-RAY DIFFRACTION	r_angle_other_deg	0.716	3	35537
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.392	5	2129
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.891	24.172	851
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.408	15	2827
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.581	15	120
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	2635
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	19328
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3640
X-RAY DIFFRACTION	r_nbd_refined	0.175	0.2	2968
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	15403
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	8231
X-RAY DIFFRACTION	r_nbtor_other	0.081	0.2	9992
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	1458
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.081	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.244	0.2	49
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.19	0.2	25
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	0.352	1.5	13508
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.417	2	17036
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.675	3	8384
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.981	4.5	6703
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	655	tight positional	0.03	0.08
1	2	C	655	tight positional	0.04	0.08
1	3	E	655	tight positional	0.04	0.08
1	4	F	655	tight positional	0.03	0.08
1	5	H	655	tight positional	0.04	0.08
1	6	J	655	tight positional	0.04	0.08
2	1	B	1667	tight positional	0.02	0.08
3	1	D	1315	tight positional	0.02	0.08
1	1	A	1321	medium positional	0.12	0.25
1	2	C	1321	medium positional	0.14	0.25
1	3	E	1321	medium positional	0.14	0.25
1	4	F	1321	medium positional	0.13	0.25
1	5	H	1321	medium positional	0.14	0.25
1	6	J	1321	medium positional	0.15	0.25
2	1	B	641	medium positional	0.19	0.25
3	1	D	1002	medium positional	0.17	0.25
1	1	A	697	loose positional	0.53	3
1	2	C	697	loose positional	0.51	3
1	3	E	697	loose positional	0.61	3
1	4	F	697	loose positional	0.6	3
1	5	H	697	loose positional	0.49	3
1	6	J	697	loose positional	0.59	3
2	1	B	473	loose positional	0.5	3
3	1	D	347	loose positional	0.73	3
1	1	A	655	tight thermal	0.28	2
1	2	C	655	tight thermal	0.21	2
1	3	E	655	tight thermal	0.22	2
1	4	F	655	tight thermal	0.19	2
1	5	H	655	tight thermal	0.18	2
1	6	J	655	tight thermal	0.17	2
2	1	B	1667	tight thermal	0.21	2
3	1	D	1315	tight thermal	0.13	2
1	1	A	1321	medium thermal	0.38	3
1	2	C	1321	medium thermal	0.31	3
1	3	E	1321	medium thermal	0.33	3
1	4	F	1321	medium thermal	0.3	3
1	5	H	1321	medium thermal	0.25	3
1	6	J	1321	medium thermal	0.24	3
2	1	B	641	medium thermal	0.41	3
3	1	D	1002	medium thermal	0.17	3
1	1	A	697	loose thermal	0.52	5
1	2	C	697	loose thermal	0.45	5
1	3	E	697	loose thermal	0.48	5
1	4	F	697	loose thermal	0.38	5
1	5	H	697	loose thermal	0.36	5
1	6	J	697	loose thermal	0.42	5
2	1	B	473	loose thermal	0.61	5
3	1	D	347	loose thermal	0.22	5

LS refinement shell

Resolution: 2.05→2.1 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.337	385
R_work	0.308	12038

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	1.101	0.1712	-0.4849	2.5049	0.1577	1.6582	-0.0228	0.0009	0.1029	0.0825	0.039	-0.2884	-0.3591	0.2155	-0.0163	-0.1738	-0.0543	-0.0198	-0.1094	0.032	-0.0855	-0.3462	20.0197	-11.2476
2	1.7383	-0.5743	-0.4447	2.282	-0.2202	1.4187	0.0574	-0.0473	0.1372	-0.0249	-0.0999	-0.4503	0.0007	0.3636	0.0425	-0.2602	-0.0477	0.0089	-0.0169	0.0003	-0.0792	11.4692	-2.9275	-19.423
3	1.5418	-0.2559	-0.1507	1.0555	-0.5612	2.3012	0.0109	-0.079	-0.1817	0.128	-0.0359	-0.1791	0.3457	0.3824	0.025	-0.1138	0.041	-0.0156	-0.1052	-0.0143	-0.0505	7.6807	-21.6676	-0.7923
4	1.1551	-0.6662	0.1537	2.03	-0.2565	2.3311	-0.0662	-0.0981	0.1116	0.4014	0.0613	-0.0817	0.0598	0.0919	0.0048	-0.1594	-0.0069	0.0213	-0.1603	0.0117	-0.1495	-5.8257	-10.1163	19.6639
5	0.4246	-0.3066	0.1735	2.0755	-0.0405	2.6468	-0.0863	-0.0171	0.1336	0.2743	0.0666	-0.0848	-0.4084	0.1172	0.0197	-0.1201	-0.0142	0.0014	-0.1362	-0.0068	-0.1041	-10.5861	15.5819	12.8681
6	1.8184	-0.6701	0.1123	1.488	-0.2971	2.0425	0.0543	-0.0784	-0.0199	-0.0233	0.0054	0.2588	-0.0789	-0.4006	-0.0597	-0.1266	-0.0035	0.0209	-0.0735	-0.0223	-0.1088	-40.6007	52.8488	69.123
7	1.4504	-0.0251	-0.4965	2.3398	-0.3478	1.7397	-0.0048	0.0556	-0.1538	-0.009	0.0205	0.402	0.2149	-0.3525	-0.0157	-0.0662	-0.0495	0.011	-0.0743	0.0209	-0.0985	-37.6508	27.4404	77.7154
8	1.307	0.3334	-0.5988	1.5065	0.1175	2.2595	-0.0163	0.1745	-0.2597	-0.1419	-0.01	0.1114	0.584	-0.1804	0.0263	0.1442	0.0198	-0.017	-0.1227	0.0093	-0.0517	-25.0642	13.4132	58.4386
9	0.949	-0.1967	-0.1366	2.1516	0.2493	2.2657	0.0872	0.147	-0.0013	-0.2777	-0.094	0.1338	0.1319	-0.0167	0.0068	-0.0146	0.0658	0.0353	-0.1514	0.005	-0.1593	-19.7413	30.4989	38.1763
10	0.7572	-0.7712	-0.0761	1.4737	-0.1204	2.3323	0.0946	0.0421	0.054	-0.1388	-0.0608	0.1137	-0.2026	-0.2015	-0.0338	-0.0487	0.0245	0.03	-0.1494	0.0113	-0.121	-29.2894	54.5369	44.7518

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 208
2	X-RAY DIFFRACTION	2	B	0 - 208
3	X-RAY DIFFRACTION	3	C	2 - 208
4	X-RAY DIFFRACTION	4	D	0 - 208
5	X-RAY DIFFRACTION	5	E	-1 - 208
6	X-RAY DIFFRACTION	6	F	2 - 208
7	X-RAY DIFFRACTION	7	G	1 - 208
8	X-RAY DIFFRACTION	8	H	1 - 207
9	X-RAY DIFFRACTION	9	I	0 - 208
10	X-RAY DIFFRACTION	10	J	2 - 208

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