PDB-4ykp: Mnemiopsis leidyi ML032222a iGluR LBD serine complex

ID or keywords:

Entry

Database: PDB / ID: 4ykp

Title

Mnemiopsis leidyi ML032222a iGluR LBD serine complex

Components

ML032222a iGluR

Keywords

MEMBRANE PROTEIN / Glutamate Receptor / Ion Channel

Function / homology

Function and homology information

ligand-gated monoatomic ion channel activity / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Mnemiopsis leidyi (sea walnut)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.46 Å

Authors

Alberstein, R.G. / Mayer, M.L.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes.
Authors: Alberstein, R. / Grey, R. / Zimmet, A. / Simmons, D.K. / Mayer, M.L.

History

Deposition	Mar 4, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 28, 2015	Group: Database references
Revision 1.2	Nov 18, 2015	Group: Database references
Revision 1.3	Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_label_seq_id
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ykp.cif.gz	317.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4ykp_validation.pdf.gz	461.3 KB	Display	wwPDB validaton report
Full document	4ykp_full_validation.pdf.gz	464.2 KB	Display
Data in XML	4ykp_validation.xml.gz	28.1 KB	Display
Data in CIF	4ykp_validation.cif.gz	44 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yk/4ykp ftp://data.pdbj.org/pub/pdb/validation_reports/yk/4ykp	HTTPS FTP

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Related structure data

Related structure data	4ykiSC 4ykjC 4ykkC 4zdmC 4ykv PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cmb-d 4yki-d 4ykk-d 5ybg-1 3g3g-d 3ijx-1 4ykj-d 3ijx-2 2xx8-2 4x48-1 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	#235 - Jul 2019 AMPA Receptor similarity (6) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: ML032222a iGluR

B: ML032222a iGluR

hetero molecules

58.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	45.862, 123.420, 54.258
Angle α, β, γ (deg.)	90.00, 112.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ML032222a iGluR Mass: 28961.559 Da / Num. of mol.: 2 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Details: The construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain connected by a synthetic GT linker Source: (gene. exp.) Mnemiopsis leidyi (sea walnut) / Gene: ML032222a / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: A0A0R4I973*PLUS
#2: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#3: Chemical	ChemComp-SER / SERINE Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	The construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain ...The construct contains residues K409-E526 and T682-S815 of the ML032222a ligand binding domain connected by a synthetic GT linker

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.24 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Reservoir: 23% PEG 8K, 100 mM Cacodylate, 150 mM MgS04. Protein buffer: 100 mM NaCl, 10 mM HEPES, pH 7.0, 0.5 mM EDTA, 100 mM serine, no added glycine PH range: 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.46→40 Å / Num. obs: 92758 / % possible obs: 95 % / Redundancy: 3.5 % / R_merge(I) obs: 0.061 / Net I/σ(I): 20
Reflection shell	Resolution: 1.46→1.49 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.536 / Mean I/σ(I) obs: 2.2 / % possible all: 86.4

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4YKI

4yki

Resolution: 1.46→38.976 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 16.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1639	4632	5.05 %	Random
R_work	0.1367	87140	-	-
obs	0.1381	91772	94.56 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.46→38.976 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4006	0	25	743	4774

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4274
X-RAY DIFFRACTION	f_angle_d	1.256	5776
X-RAY DIFFRACTION	f_dihedral_angle_d	12.953	1578
X-RAY DIFFRACTION	f_chiral_restr	0.074	614
X-RAY DIFFRACTION	f_plane_restr	0.006	761

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.4578-1.4743	0.2411	128	0.2245	2318	X-RAY DIFFRACTION	75
1.4743-1.4917	0.2483	137	0.2173	2672	X-RAY DIFFRACTION	88
1.4917-1.5099	0.2276	151	0.2017	2723	X-RAY DIFFRACTION	89
1.5099-1.529	0.1893	137	0.1863	2764	X-RAY DIFFRACTION	89
1.529-1.5491	0.2229	149	0.1749	2766	X-RAY DIFFRACTION	90
1.5491-1.5703	0.194	153	0.1722	2756	X-RAY DIFFRACTION	91
1.5703-1.5928	0.2113	155	0.1691	2776	X-RAY DIFFRACTION	90
1.5928-1.6166	0.2061	130	0.1615	2815	X-RAY DIFFRACTION	92
1.6166-1.6418	0.1714	156	0.154	2830	X-RAY DIFFRACTION	91
1.6418-1.6687	0.1756	151	0.1545	2824	X-RAY DIFFRACTION	94
1.6687-1.6975	0.1785	160	0.1571	2893	X-RAY DIFFRACTION	92
1.6975-1.7284	0.1803	156	0.1502	2822	X-RAY DIFFRACTION	94
1.7284-1.7616	0.2047	147	0.149	2928	X-RAY DIFFRACTION	94
1.7616-1.7976	0.1688	154	0.142	2885	X-RAY DIFFRACTION	95
1.7976-1.8367	0.1641	164	0.141	2920	X-RAY DIFFRACTION	95
1.8367-1.8794	0.1635	153	0.1452	2952	X-RAY DIFFRACTION	96
1.8794-1.9264	0.1435	158	0.1384	2945	X-RAY DIFFRACTION	96
1.9264-1.9785	0.1555	145	0.129	2995	X-RAY DIFFRACTION	97
1.9785-2.0367	0.1589	161	0.1317	3002	X-RAY DIFFRACTION	98
2.0367-2.1024	0.1518	163	0.1235	2987	X-RAY DIFFRACTION	97
2.1024-2.1776	0.1566	146	0.1252	3056	X-RAY DIFFRACTION	98
2.1776-2.2647	0.1453	162	0.1268	3007	X-RAY DIFFRACTION	99
2.2647-2.3678	0.1666	139	0.1272	3059	X-RAY DIFFRACTION	99
2.3678-2.4926	0.1761	149	0.1294	3029	X-RAY DIFFRACTION	99
2.4926-2.6487	0.1724	162	0.1355	3050	X-RAY DIFFRACTION	99
2.6487-2.8532	0.1673	166	0.1403	3074	X-RAY DIFFRACTION	99
2.8532-3.1402	0.1529	155	0.1349	3078	X-RAY DIFFRACTION	100
3.1402-3.5943	0.1441	165	0.124	3063	X-RAY DIFFRACTION	100
3.5943-4.5274	0.1417	177	0.1096	3087	X-RAY DIFFRACTION	100
4.5274-38.9895	0.1653	203	0.1423	3064	X-RAY DIFFRACTION	99

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	1.3147	-0.2908	0.0362	1.017	-0.6863	0.5792	0.069	-0.0601	-0.145	-0.012	-0.025	-0.0309	0.1253	0.0944	-0.0418	0.1117	0.0039	-0.0111	0.1273	0.0073	0.1746	20.4449	54.3678	50.7059
2	0.8898	0.0711	0.3714	0.8901	0.5517	1.7118	-0.0021	-0.0183	0.0079	0.0609	-0.0347	-0.1913	0.0397	0.224	0.0117	0.1047	0.0129	-0.0273	0.1349	0.0132	0.1829	26.125	57.8547	51.7624
3	1.8019	0.087	0.4871	1.5194	0.0149	1.7767	-0.01	-0.1808	-0.0794	0.0654	0.0011	0.1792	0.095	-0.1719	0.0144	0.105	-0.0115	0.0015	0.1259	0.0118	0.1724	5.8815	56.5284	55.8755
4	2.1626	0.2336	0.4236	0.3862	0.1226	1.1364	-0.0615	0.3916	-0.1054	-0.1349	0.0176	0.0275	0.0087	-0.031	0.0657	0.1538	-0.0047	-0.0161	0.1673	-0.0222	0.1782	2.7754	60.9322	37.2284
5	1.1957	0.1805	-0.9555	1.2845	-0.4108	4.0002	0.0069	-0.1415	0.0622	0.1424	-0.0214	-0.1051	-0.0663	-0.0652	0.0541	0.1061	-0.003	-0.0333	0.1331	0.0168	0.1608	22.9553	71.9434	51.9728
6	6.5641	-1.104	0.4187	6.0287	-0.7881	3.8366	-0.3375	0.6594	-0.0842	-0.4449	0.0746	0.093	0.0099	-0.028	0.2265	0.1504	-0.0344	-0.0019	0.2235	-0.0128	0.1637	24.2957	62.3526	35.6437
7	2.1203	0.1315	-0.8869	0.5424	0.5998	2.5188	-0.0165	-0.0953	-0.0988	0.0693	0.0139	0.0451	0.1645	-0.0468	0.0428	0.1011	0.0095	-0.0216	0.0938	0.0086	0.1049	7.1186	91.0313	53.4394
8	1.1665	0.0162	-0.1142	2.5377	0.3886	1.3203	0.0289	0.0819	0.1568	0.0147	-0.0031	-0.0902	-0.2168	-0.1533	-0.0119	0.1178	0.029	-0.0153	0.1248	0.0049	0.1174	4.3108	99.1323	44.7107
9	1.495	0.0538	-0.504	1.0131	0.0797	1.2328	-0.0046	-0.133	0.0403	0.0421	0.0156	-0.054	-0.0524	0.0906	-0.0103	0.0842	0.0008	-0.0184	0.0891	-0.003	0.0826	15.526	93.4855	53.6045
10	1.0003	0.1457	-0.8337	0.1955	-0.2697	1.6371	-0.0133	0.0922	-0.0686	-0.0451	-0.0077	-0.0244	0.0128	0.0224	0.0206	0.0966	-0.0043	-0.02	0.1064	-0.0109	0.0991	24.8999	88.4858	36.0703
11	0.9046	-0.0512	0.7116	0.7092	0.123	2.9234	0.0269	0.0532	-0.1717	0.0391	-0.0239	0.0944	0.1908	0.0153	0.044	0.0914	-0.0056	-0.0067	0.1185	-0.0144	0.1514	4.4811	79.3878	50.1314
12	2.2271	0.4586	-1.7856	0.4449	-0.4646	1.4483	-0.192	1.0341	0.1156	-0.4565	0.0625	-0.1841	-0.1987	0.059	0.0304	0.2146	-0.0283	-0.0138	0.4438	0.0059	0.1554	5.4494	88.9135	29.2171

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:28)
2	X-RAY DIFFRACTION	2	(chain A and resid 29:55)
3	X-RAY DIFFRACTION	3	(chain A and resid 56:88)
4	X-RAY DIFFRACTION	4	(chain A and resid 89:220)
5	X-RAY DIFFRACTION	5	(chain A and resid 221:241)
6	X-RAY DIFFRACTION	6	(chain A and resid 242:251)
7	X-RAY DIFFRACTION	7	(chain B and resid 1:21)
8	X-RAY DIFFRACTION	8	(chain B and resid 22:41)
9	X-RAY DIFFRACTION	9	(chain B and resid 42:86)
10	X-RAY DIFFRACTION	10	(chain B and resid 87:220)
11	X-RAY DIFFRACTION	11	(chain B and resid 221:244)
12	X-RAY DIFFRACTION	12	(chain B and resid 245:255)

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