PDB-5oal: Crystal structure of mutant AChBP in complex with strychnine (T53...

ID or keywords:

Entry

Database: PDB / ID: 5oal

Title

Crystal structure of mutant AChBP in complex with strychnine (T53F, Q74R, Y110A, I135S, G162E)

Components

Soluble acetylcholine receptor

Keywords

SIGNALING PROTEIN / receptor / acetylcholine binding

Function / homology

Function and homology information

acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding
Similarity search - Function

Biological species

Aplysia californica (California sea hare)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Dawson, A. / Hunter, W.N. / de Souza, J.O. / Trumper, P.

Citation

Journal: Iucrj / Year: 2019
Title: Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein.
Authors: Dawson, A. / Trumper, P. / de Souza, J.O. / Parker, H. / Jones, M.J. / Hales, T.G. / Hunter, W.N.

History

Deposition	Jun 22, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 1, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5oal.cif.gz	627.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5oal.ent.gz	515 KB	Display	PDB format
PDBx/mmJSON format	5oal.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5oal_validation.pdf.gz	4.7 MB	Display	wwPDB validaton report
Full document	5oal_full_validation.pdf.gz	4.8 MB	Display
Data in XML	5oal_validation.xml.gz	105.1 KB	Display
Data in CIF	5oal_validation.cif.gz	136.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/5oal ftp://data.pdbj.org/pub/pdb/validation_reports/oa/5oal	HTTPS FTP

-
Related structure data

Related structure data	5o87C 5o8tC 5oa0C 5oadC 5oajC 5oanC 5obgC 2xysS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xys-d 5ain-d 2w8g-d 2w8f-1 2y58-d 2xyt-1 5lxb-1 2xnu-d 2br7-d 5o8t-d 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (5) #71 - Nov 2005 Acetylcholine Receptor similarity (4) #133 - Jan 2011 Nitric Oxide Synthase similarity (1)

Deposited unit

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

K: Soluble acetylcholine receptor

L: Soluble acetylcholine receptor

M: Soluble acetylcholine receptor

N: Soluble acetylcholine receptor

O: Soluble acetylcholine receptor

hetero molecules

431 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

hetero molecules

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

2

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

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

3

K: Soluble acetylcholine receptor

L: Soluble acetylcholine receptor

M: Soluble acetylcholine receptor

N: Soluble acetylcholine receptor

O: Soluble acetylcholine receptor

hetero molecules

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

Unit cell

Length a, b, c (Å)	130.900, 130.900, 190.139
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	A	A	20 - 224	20 - 224
2	1	ARG	ARG	B	B	20 - 224	20 - 224
1	2	ARG	ARG	A	A	20 - 224	20 - 224
2	2	ARG	ARG	C	C	20 - 224	20 - 224
1	3	ARG	ARG	A	A	20 - 225	20 - 225
2	3	ARG	ARG	D	D	20 - 225	20 - 225
1	4	ARG	ARG	A	A	20 - 222	20 - 222
2	4	ARG	ARG	E	E	20 - 222	20 - 222
1	5	ARG	ARG	A	A	20 - 225	20 - 225
2	5	ARG	ARG	F	F	20 - 225	20 - 225
1	6	ARG	ARG	A	A	20 - 225	20 - 225
2	6	ARG	ARG	G	G	20 - 225	20 - 225
1	7	ARG	ARG	A	A	20 - 225	20 - 225
2	7	ARG	ARG	H	H	20 - 225	20 - 225
1	8	ARG	ARG	A	A	20 - 225	20 - 225
2	8	ARG	ARG	I	I	20 - 225	20 - 225
1	9	ARG	ARG	A	A	20 - 225	20 - 225
2	9	ARG	ARG	J	J	20 - 225	20 - 225
1	10	ARG	ARG	A	A	20 - 225	20 - 225
2	10	ARG	ARG	K	K	20 - 225	20 - 225
1	11	ARG	ARG	A	A	20 - 225	20 - 225
2	11	ARG	ARG	L	L	20 - 225	20 - 225
1	12	ARG	ARG	A	A	20 - 225	20 - 225
2	12	ARG	ARG	M	M	20 - 225	20 - 225
1	13	ARG	ARG	A	A	20 - 224	20 - 224
2	13	ARG	ARG	N	N	20 - 224	20 - 224
1	14	ARG	ARG	A	A	20 - 225	20 - 225
2	14	ARG	ARG	O	O	20 - 225	20 - 225
1	15	ALA	ALA	B	B	20 - 226	20 - 226
2	15	ALA	ALA	C	C	20 - 226	20 - 226
1	16	ARG	ARG	B	B	20 - 224	20 - 224
2	16	ARG	ARG	D	D	20 - 224	20 - 224
1	17	ARG	ARG	B	B	20 - 222	20 - 222
2	17	ARG	ARG	E	E	20 - 222	20 - 222
1	18	ARG	ARG	B	B	20 - 224	20 - 224
2	18	ARG	ARG	F	F	20 - 224	20 - 224
1	19	ARG	ARG	B	B	20 - 225	20 - 225
2	19	ARG	ARG	G	G	20 - 225	20 - 225
1	20	ARG	ARG	B	B	20 - 224	20 - 224
2	20	ARG	ARG	H	H	20 - 224	20 - 224
1	21	ARG	ARG	B	B	20 - 224	20 - 224
2	21	ARG	ARG	I	I	20 - 224	20 - 224
1	22	ARG	ARG	B	B	20 - 224	20 - 224
2	22	ARG	ARG	J	J	20 - 224	20 - 224
1	23	ARG	ARG	B	B	20 - 224	20 - 224
2	23	ARG	ARG	K	K	20 - 224	20 - 224
1	24	ARG	ARG	B	B	20 - 224	20 - 224
2	24	ARG	ARG	L	L	20 - 224	20 - 224
1	25	ARG	ARG	B	B	20 - 224	20 - 224
2	25	ARG	ARG	M	M	20 - 224	20 - 224
1	26	ARG	ARG	B	B	20 - 224	20 - 224
2	26	ARG	ARG	N	N	20 - 224	20 - 224
1	27	ARG	ARG	B	B	20 - 224	20 - 224
2	27	ARG	ARG	O	O	20 - 224	20 - 224
1	28	ARG	ARG	C	C	20 - 224	20 - 224
2	28	ARG	ARG	D	D	20 - 224	20 - 224
1	29	ARG	ARG	C	C	20 - 222	20 - 222
2	29	ARG	ARG	E	E	20 - 222	20 - 222
1	30	ARG	ARG	C	C	20 - 224	20 - 224
2	30	ARG	ARG	F	F	20 - 224	20 - 224
1	31	ARG	ARG	C	C	20 - 225	20 - 225
2	31	ARG	ARG	G	G	20 - 225	20 - 225
1	32	ARG	ARG	C	C	20 - 224	20 - 224
2	32	ARG	ARG	H	H	20 - 224	20 - 224
1	33	ARG	ARG	C	C	20 - 224	20 - 224
2	33	ARG	ARG	I	I	20 - 224	20 - 224
1	34	ARG	ARG	C	C	20 - 224	20 - 224
2	34	ARG	ARG	J	J	20 - 224	20 - 224
1	35	ARG	ARG	C	C	20 - 224	20 - 224
2	35	ARG	ARG	K	K	20 - 224	20 - 224
1	36	ARG	ARG	C	C	20 - 224	20 - 224
2	36	ARG	ARG	L	L	20 - 224	20 - 224
1	37	ARG	ARG	C	C	20 - 224	20 - 224
2	37	ARG	ARG	M	M	20 - 224	20 - 224
1	38	ARG	ARG	C	C	20 - 224	20 - 224
2	38	ARG	ARG	N	N	20 - 224	20 - 224
1	39	ARG	ARG	C	C	20 - 224	20 - 224
2	39	ARG	ARG	O	O	20 - 224	20 - 224
1	40	ARG	ARG	D	D	20 - 222	20 - 222
2	40	ARG	ARG	E	E	20 - 222	20 - 222
1	41	ARG	ARG	D	D	20 - 225	20 - 225
2	41	ARG	ARG	F	F	20 - 225	20 - 225
1	42	ARG	ARG	D	D	20 - 225	20 - 225
2	42	ARG	ARG	G	G	20 - 225	20 - 225
1	43	ARG	ARG	D	D	20 - 225	20 - 225
2	43	ARG	ARG	H	H	20 - 225	20 - 225
1	44	ARG	ARG	D	D	20 - 225	20 - 225
2	44	ARG	ARG	I	I	20 - 225	20 - 225
1	45	ARG	ARG	D	D	20 - 225	20 - 225
2	45	ARG	ARG	J	J	20 - 225	20 - 225
1	46	ARG	ARG	D	D	20 - 225	20 - 225
2	46	ARG	ARG	K	K	20 - 225	20 - 225
1	47	ARG	ARG	D	D	20 - 225	20 - 225
2	47	ARG	ARG	L	L	20 - 225	20 - 225
1	48	ARG	ARG	D	D	20 - 225	20 - 225
2	48	ARG	ARG	M	M	20 - 225	20 - 225
1	49	ARG	ARG	D	D	20 - 224	20 - 224
2	49	ARG	ARG	N	N	20 - 224	20 - 224
1	50	ARG	ARG	D	D	20 - 225	20 - 225
2	50	ARG	ARG	O	O	20 - 225	20 - 225
1	51	ARG	ARG	E	E	20 - 222	20 - 222
2	51	ARG	ARG	F	F	20 - 222	20 - 222
1	52	GLU	GLU	E	E	20 - 223	20 - 223
2	52	GLU	GLU	G	G	20 - 223	20 - 223
1	53	ARG	ARG	E	E	20 - 222	20 - 222
2	53	ARG	ARG	H	H	20 - 222	20 - 222
1	54	ARG	ARG	E	E	20 - 222	20 - 222
2	54	ARG	ARG	I	I	20 - 222	20 - 222
1	55	ARG	ARG	E	E	20 - 222	20 - 222
2	55	ARG	ARG	J	J	20 - 222	20 - 222
1	56	ARG	ARG	E	E	20 - 222	20 - 222
2	56	ARG	ARG	K	K	20 - 222	20 - 222
1	57	ARG	ARG	E	E	20 - 222	20 - 222
2	57	ARG	ARG	L	L	20 - 222	20 - 222
1	58	ARG	ARG	E	E	20 - 222	20 - 222
2	58	ARG	ARG	M	M	20 - 222	20 - 222
1	59	GLU	GLU	E	E	20 - 223	20 - 223
2	59	GLU	GLU	N	N	20 - 223	20 - 223
1	60	ARG	ARG	E	E	20 - 222	20 - 222
2	60	ARG	ARG	O	O	20 - 222	20 - 222
1	61	ARG	ARG	F	F	20 - 225	20 - 225
2	61	ARG	ARG	G	G	20 - 225	20 - 225
1	62	ARG	ARG	F	F	20 - 225	20 - 225
2	62	ARG	ARG	H	H	20 - 225	20 - 225
1	63	ARG	ARG	F	F	20 - 225	20 - 225
2	63	ARG	ARG	I	I	20 - 225	20 - 225
1	64	ARG	ARG	F	F	20 - 225	20 - 225
2	64	ARG	ARG	J	J	20 - 225	20 - 225
1	65	ARG	ARG	F	F	20 - 225	20 - 225
2	65	ARG	ARG	K	K	20 - 225	20 - 225
1	66	ARG	ARG	F	F	20 - 225	20 - 225
2	66	ARG	ARG	L	L	20 - 225	20 - 225
1	67	ARG	ARG	F	F	20 - 225	20 - 225
2	67	ARG	ARG	M	M	20 - 225	20 - 225
1	68	ARG	ARG	F	F	20 - 224	20 - 224
2	68	ARG	ARG	N	N	20 - 224	20 - 224
1	69	ARG	ARG	F	F	20 - 225	20 - 225
2	69	ARG	ARG	O	O	20 - 225	20 - 225
1	70	ARG	ARG	G	G	20 - 225	20 - 225
2	70	ARG	ARG	H	H	20 - 225	20 - 225
1	71	ARG	ARG	G	G	20 - 225	20 - 225
2	71	ARG	ARG	I	I	20 - 225	20 - 225
1	72	ARG	ARG	G	G	20 - 225	20 - 225
2	72	ARG	ARG	J	J	20 - 225	20 - 225
1	73	ARG	ARG	G	G	20 - 225	20 - 225
2	73	ARG	ARG	K	K	20 - 225	20 - 225
1	74	ARG	ARG	G	G	20 - 225	20 - 225
2	74	ARG	ARG	L	L	20 - 225	20 - 225
1	75	ARG	ARG	G	G	20 - 225	20 - 225
2	75	ARG	ARG	M	M	20 - 225	20 - 225
1	76	GLU	GLU	G	G	20 - 223	20 - 223
2	76	GLU	GLU	N	N	20 - 223	20 - 223
1	77	ARG	ARG	G	G	20 - 225	20 - 225
2	77	ARG	ARG	O	O	20 - 225	20 - 225
1	78	ARG	ARG	H	H	20 - 225	20 - 225
2	78	ARG	ARG	I	I	20 - 225	20 - 225
1	79	ARG	ARG	H	H	20 - 225	20 - 225
2	79	ARG	ARG	J	J	20 - 225	20 - 225
1	80	ARG	ARG	H	H	20 - 225	20 - 225
2	80	ARG	ARG	K	K	20 - 225	20 - 225
1	81	ARG	ARG	H	H	20 - 225	20 - 225
2	81	ARG	ARG	L	L	20 - 225	20 - 225
1	82	ARG	ARG	H	H	20 - 225	20 - 225
2	82	ARG	ARG	M	M	20 - 225	20 - 225
1	83	ARG	ARG	H	H	20 - 224	20 - 224
2	83	ARG	ARG	N	N	20 - 224	20 - 224
1	84	ARG	ARG	H	H	20 - 225	20 - 225
2	84	ARG	ARG	O	O	20 - 225	20 - 225
1	85	ARG	ARG	I	I	20 - 225	20 - 225
2	85	ARG	ARG	J	J	20 - 225	20 - 225
1	86	ARG	ARG	I	I	20 - 225	20 - 225
2	86	ARG	ARG	K	K	20 - 225	20 - 225
1	87	ARG	ARG	I	I	20 - 225	20 - 225
2	87	ARG	ARG	L	L	20 - 225	20 - 225
1	88	ARG	ARG	I	I	20 - 225	20 - 225
2	88	ARG	ARG	M	M	20 - 225	20 - 225
1	89	ARG	ARG	I	I	20 - 224	20 - 224
2	89	ARG	ARG	N	N	20 - 224	20 - 224
1	90	ARG	ARG	I	I	20 - 225	20 - 225
2	90	ARG	ARG	O	O	20 - 225	20 - 225
1	91	ARG	ARG	J	J	20 - 225	20 - 225
2	91	ARG	ARG	K	K	20 - 225	20 - 225
1	92	ARG	ARG	J	J	20 - 225	20 - 225
2	92	ARG	ARG	L	L	20 - 225	20 - 225
1	93	ARG	ARG	J	J	20 - 225	20 - 225
2	93	ARG	ARG	M	M	20 - 225	20 - 225
1	94	ARG	ARG	J	J	20 - 224	20 - 224
2	94	ARG	ARG	N	N	20 - 224	20 - 224
1	95	ARG	ARG	J	J	20 - 225	20 - 225
2	95	ARG	ARG	O	O	20 - 225	20 - 225
1	96	ARG	ARG	K	K	20 - 225	20 - 225
2	96	ARG	ARG	L	L	20 - 225	20 - 225
1	97	ARG	ARG	K	K	20 - 225	20 - 225
2	97	ARG	ARG	M	M	20 - 225	20 - 225
1	98	ARG	ARG	K	K	20 - 224	20 - 224
2	98	ARG	ARG	N	N	20 - 224	20 - 224
1	99	ARG	ARG	K	K	20 - 225	20 - 225
2	99	ARG	ARG	O	O	20 - 225	20 - 225
1	100	ARG	ARG	L	L	20 - 225	20 - 225
2	100	ARG	ARG	M	M	20 - 225	20 - 225
1	101	ARG	ARG	L	L	20 - 224	20 - 224
2	101	ARG	ARG	N	N	20 - 224	20 - 224
1	102	ARG	ARG	L	L	20 - 225	20 - 225
2	102	ARG	ARG	O	O	20 - 225	20 - 225
1	103	ARG	ARG	M	M	20 - 224	20 - 224
2	103	ARG	ARG	N	N	20 - 224	20 - 224
1	104	ARG	ARG	M	M	20 - 225	20 - 225
2	104	ARG	ARG	O	O	20 - 225	20 - 225
1	105	ARG	ARG	N	N	20 - 224	20 - 224
2	105	ARG	ARG	O	O	20 - 224	20 - 224

NCS ensembles :

#1: Protein	Soluble acetylcholine receptor Mass: 28355.773 Da / Num. of mol.: 15 / Mutation: T53F, Q74R, Y110A, I135S, G162E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aplysia californica (California sea hare) Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q8WSF8
#2: Chemical	ChemComp-SY9 / STRYCHNINE Mass: 334.412 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₂₁H₂₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#3: Chemical	ChemComp-ARG / ARGININE Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Reservoir buffer: 20 % PEG3350 0.2 M Mg formate Protein buffer: 50 mM trism 250 mM NaCl Ph 7.5, 0.5 mM strychnine

-
Data collection

Diffraction	Mean temperature: 150 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97627 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2015
Radiation	Monochromator: Al filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97627 Å / Relative weight: 1
Reflection	Resolution: 3.2→72.85 Å / Num. obs: 59286 / % possible obs: 98.7 % / Redundancy: 8.1 % / B_iso Wilson estimate: 51.7 Å² / CC_1/2: 0.991 / R_merge(I) obs: 0.212 / Net I/σ(I): 8.3
Reflection shell	Resolution: 3.2→3.29 Å / Redundancy: 7.3 % / R_merge(I) obs: 1.073 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4605 / CC_1/2: 0.691 / % possible all: 98.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2xys

2xys

Resolution: 3.2→72.85 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.894 / SU B: 26.716 / SU ML: 0.425 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23053	2910	4.9 %	RANDOM
R_work	0.18764	-	-	-
obs	0.1898	56374	98.58 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 77.086 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.81 Å²	1.41 Å²	0 Å²
2-	-	2.81 Å²	0 Å²
3-	-	-	-9.13 Å²

Refinement step

Cycle: 1 / Resolution: 3.2→72.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24623	0	386	0	25009

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	25722
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	22769
X-RAY DIFFRACTION	r_angle_refined_deg	2.053	1.932	35205
X-RAY DIFFRACTION	r_angle_other_deg	1.111	3	53039
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.443	5	3061
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.341	24.235	1209
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.865	15	4119
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.132	15	162
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	3933
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	28906
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5292
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	8.915	7.533	12298
X-RAY DIFFRACTION	r_mcbond_other	8.913	7.533	12297
X-RAY DIFFRACTION	r_mcangle_it	13.441	11.282	15341
X-RAY DIFFRACTION	r_mcangle_other	13.441	11.283	15342
X-RAY DIFFRACTION	r_scbond_it	9.451	8.166	13424
X-RAY DIFFRACTION	r_scbond_other	9.448	8.166	13424
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	14.029	12.006	19865
X-RAY DIFFRACTION	r_long_range_B_refined	17.661	87.483	27374
X-RAY DIFFRACTION	r_long_range_B_other	17.661	87.487	27375
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	13142	0.05
1	2	B	13142	0.05
2	1	A	13200	0.05
2	2	C	13200	0.05
3	1	A	13226	0.05
3	2	D	13226	0.05
4	1	A	12968	0.04
4	2	E	12968	0.04
5	1	A	13252	0.05
5	2	F	13252	0.05
6	1	A	13038	0.04
6	2	G	13038	0.04
7	1	A	13356	0.04
7	2	H	13356	0.04
8	1	A	13220	0.06
8	2	I	13220	0.06
9	1	A	13236	0.04
9	2	J	13236	0.04
10	1	A	13264	0.05
10	2	K	13264	0.05
11	1	A	13222	0.05
11	2	L	13222	0.05
12	1	A	13202	0.04
12	2	M	13202	0.04
13	1	A	12784	0.05
13	2	N	12784	0.05
14	1	A	13254	0.05
14	2	O	13254	0.05
15	1	B	13350	0.05
15	2	C	13350	0.05
16	1	B	13206	0.05
16	2	D	13206	0.05
17	1	B	13000	0.05
17	2	E	13000	0.05
18	1	B	13180	0.05
18	2	F	13180	0.05
19	1	B	13014	0.05
19	2	G	13014	0.05
20	1	B	13214	0.05
20	2	H	13214	0.05
21	1	B	13142	0.06
21	2	I	13142	0.06
22	1	B	13184	0.05
22	2	J	13184	0.05
23	1	B	13152	0.05
23	2	K	13152	0.05
24	1	B	13232	0.03
24	2	L	13232	0.03
25	1	B	13188	0.04
25	2	M	13188	0.04
26	1	B	12758	0.05
26	2	N	12758	0.05
27	1	B	13272	0.04
27	2	O	13272	0.04
28	1	C	13216	0.05
28	2	D	13216	0.05
29	1	C	13052	0.04
29	2	E	13052	0.04
30	1	C	13206	0.05
30	2	F	13206	0.05
31	1	C	13050	0.05
31	2	G	13050	0.05
32	1	C	13276	0.04
32	2	H	13276	0.04
33	1	C	13192	0.05
33	2	I	13192	0.05
34	1	C	13220	0.04
34	2	J	13220	0.04
35	1	C	13206	0.04
35	2	K	13206	0.04
36	1	C	13226	0.04
36	2	L	13226	0.04
37	1	C	13230	0.03
37	2	M	13230	0.03
38	1	C	12834	0.04
38	2	N	12834	0.04
39	1	C	13234	0.05
39	2	O	13234	0.05
40	1	D	13062	0.04
40	2	E	13062	0.04
41	1	D	13214	0.05
41	2	F	13214	0.05
42	1	D	13036	0.05
42	2	G	13036	0.05
43	1	D	13270	0.05
43	2	H	13270	0.05
44	1	D	13214	0.06
44	2	I	13214	0.06
45	1	D	13254	0.06
45	2	J	13254	0.06
46	1	D	13270	0.06
46	2	K	13270	0.06
47	1	D	13282	0.05
47	2	L	13282	0.05
48	1	D	13288	0.05
48	2	M	13288	0.05
49	1	D	12766	0.04
49	2	N	12766	0.04
50	1	D	13268	0.06
50	2	O	13268	0.06
51	1	E	13026	0.05
51	2	F	13026	0.05
52	1	E	12916	0.04
52	2	G	12916	0.04
53	1	E	13054	0.04
53	2	H	13054	0.04
54	1	E	12988	0.05
54	2	I	12988	0.05
55	1	E	13040	0.05
55	2	J	13040	0.05
56	1	E	13004	0.05
56	2	K	13004	0.05
57	1	E	13050	0.04
57	2	L	13050	0.04
58	1	E	13022	0.03
58	2	M	13022	0.03
59	1	E	12646	0.05
59	2	N	12646	0.05
60	1	E	13042	0.05
60	2	O	13042	0.05
61	1	F	13036	0.05
61	2	G	13036	0.05
62	1	F	13342	0.04
62	2	H	13342	0.04
63	1	F	13204	0.05
63	2	I	13204	0.05
64	1	F	13240	0.05
64	2	J	13240	0.05
65	1	F	13238	0.05
65	2	K	13238	0.05
66	1	F	13220	0.05
66	2	L	13220	0.05
67	1	F	13194	0.04
67	2	M	13194	0.04
68	1	F	12728	0.05
68	2	N	12728	0.05
69	1	F	13252	0.05
69	2	O	13252	0.05
70	1	G	13108	0.04
70	2	H	13108	0.04
71	1	G	13000	0.06
71	2	I	13000	0.06
72	1	G	13028	0.05
72	2	J	13028	0.05
73	1	G	13064	0.04
73	2	K	13064	0.04
74	1	G	13034	0.04
74	2	L	13034	0.04
75	1	G	13024	0.04
75	2	M	13024	0.04
76	1	G	12462	0.04
76	2	N	12462	0.04
77	1	G	13054	0.05
77	2	O	13054	0.05
78	1	H	13290	0.05
78	2	I	13290	0.05
79	1	H	13310	0.04
79	2	J	13310	0.04
80	1	H	13324	0.04
80	2	K	13324	0.04
81	1	H	13296	0.05
81	2	L	13296	0.05
82	1	H	13254	0.04
82	2	M	13254	0.04
83	1	H	12814	0.05
83	2	N	12814	0.05
84	1	H	13306	0.05
84	2	O	13306	0.05
85	1	I	13294	0.05
85	2	J	13294	0.05
86	1	I	13220	0.06
86	2	K	13220	0.06
87	1	I	13256	0.05
87	2	L	13256	0.05
88	1	I	13238	0.05
88	2	M	13238	0.05
89	1	I	12770	0.05
89	2	N	12770	0.05
90	1	I	13228	0.06
90	2	O	13228	0.06
91	1	J	13288	0.04
91	2	K	13288	0.04
92	1	J	13276	0.05
92	2	L	13276	0.05
93	1	J	13264	0.04
93	2	M	13264	0.04
94	1	J	12798	0.04
94	2	N	12798	0.04
95	1	J	13296	0.05
95	2	O	13296	0.05
96	1	K	13264	0.05
96	2	L	13264	0.05
97	1	K	13258	0.05
97	2	M	13258	0.05
98	1	K	12748	0.05
98	2	N	12748	0.05
99	1	K	13260	0.06
99	2	O	13260	0.06
100	1	L	13260	0.04
100	2	M	13260	0.04
101	1	L	12782	0.05
101	2	N	12782	0.05
102	1	L	13320	0.03
102	2	O	13320	0.03
103	1	M	12750	0.04
103	2	N	12750	0.04
104	1	M	13296	0.04
104	2	O	13296	0.04
105	1	N	12792	0.05
105	2	O	12792	0.05

LS refinement shell

Resolution: 3.2→3.283 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.358	198	-
R_work	0.325	4164	-
obs	-	-	98.42 %

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi