PDB-4ykj: Mnemiopsis leidyi ML032222a iGluR LBD complex with Alanine

ID or keywords:

Entry

Database: PDB / ID: 4ykj

Title

Mnemiopsis leidyi ML032222a iGluR LBD complex with Alanine

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 / membrane
Similarity search - Function

Biological species

Mnemiopsis leidyi (sea walnut)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.401 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_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Nov 6, 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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Download

PDBx/mmCIF format	4ykj.cif.gz	322.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ykj.ent.gz	268.7 KB	Display	PDB format
PDBx/mmJSON format	4ykj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yk/4ykj ftp://data.pdbj.org/pub/pdb/validation_reports/yk/4ykj	HTTPS FTP

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Related structure data

Related structure data	4ykiSC 4ykkC 4ykpC 4zdmC 4ykv PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cmc-d 4ykp-d 4yki-d 3g3j-d 4ykk-d 6faz-d 2xxi-1 4iy6-1 5cmb-d 1xhy-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

Unit cell

Length a, b, c (Å)	45.962, 123.950, 54.468
Angle α, β, γ (deg.)	90.00, 111.62, 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-ALA / ALANINE Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₂
#3: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 824 / 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: 25% 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 alanine, 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 3, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.4→40 Å / Num. obs: 110735 / % possible obs: 99.1 % / Redundancy: 3.7 % / R_merge(I) obs: 0.062 / Net I/σ(I): 19.6
Reflection shell	Resolution: 1.4→1.42 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.501 / Mean I/σ(I) obs: 1.9 / % possible all: 87.1

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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: 1.401→39.211 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1652	5540	5.05 %	Random
R_work	0.1405	-	-	-
obs	0.1418	109639	98.98 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.401→39.211 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4006	0	22	824	4852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4334
X-RAY DIFFRACTION	f_angle_d	1.246	5870
X-RAY DIFFRACTION	f_dihedral_angle_d	12.912	1612
X-RAY DIFFRACTION	f_chiral_restr	0.074	622
X-RAY DIFFRACTION	f_plane_restr	0.006	776

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 (%)
1.4011-1.417	0.2581	155	0.2497	2914	X-RAY DIFFRACTION	84
1.417-1.4337	0.2542	176	0.2331	3221	X-RAY DIFFRACTION	91
1.4337-1.4512	0.258	176	0.2078	3321	X-RAY DIFFRACTION	96
1.4512-1.4696	0.1963	180	0.1893	3515	X-RAY DIFFRACTION	100
1.4696-1.4889	0.1889	192	0.1721	3502	X-RAY DIFFRACTION	100
1.4889-1.5093	0.1921	188	0.1685	3454	X-RAY DIFFRACTION	100
1.5093-1.5309	0.1676	182	0.1608	3532	X-RAY DIFFRACTION	100
1.5309-1.5537	0.1997	183	0.1564	3478	X-RAY DIFFRACTION	100
1.5537-1.578	0.1689	195	0.1514	3497	X-RAY DIFFRACTION	100
1.578-1.6039	0.1637	199	0.1485	3513	X-RAY DIFFRACTION	100
1.6039-1.6315	0.1747	165	0.145	3517	X-RAY DIFFRACTION	100
1.6315-1.6612	0.1888	191	0.1423	3463	X-RAY DIFFRACTION	100
1.6612-1.6931	0.1621	191	0.1364	3514	X-RAY DIFFRACTION	100
1.6931-1.7277	0.1656	186	0.1348	3504	X-RAY DIFFRACTION	100
1.7277-1.7653	0.167	176	0.1406	3527	X-RAY DIFFRACTION	100
1.7653-1.8063	0.1729	184	0.1355	3463	X-RAY DIFFRACTION	100
1.8063-1.8515	0.162	196	0.1392	3501	X-RAY DIFFRACTION	100
1.8515-1.9016	0.1655	184	0.134	3508	X-RAY DIFFRACTION	100
1.9016-1.9575	0.1416	174	0.1357	3512	X-RAY DIFFRACTION	100
1.9575-2.0207	0.1677	193	0.1313	3496	X-RAY DIFFRACTION	100
2.0207-2.0929	0.145	187	0.1269	3539	X-RAY DIFFRACTION	100
2.0929-2.1767	0.1635	181	0.1285	3509	X-RAY DIFFRACTION	100
2.1767-2.2758	0.1337	181	0.1278	3495	X-RAY DIFFRACTION	100
2.2758-2.3957	0.1839	168	0.1251	3503	X-RAY DIFFRACTION	100
2.3957-2.5458	0.1645	171	0.1397	3528	X-RAY DIFFRACTION	100
2.5458-2.7423	0.1569	186	0.1381	3515	X-RAY DIFFRACTION	100
2.7423-3.0182	0.1507	185	0.1408	3526	X-RAY DIFFRACTION	100
3.0182-3.4547	0.1606	176	0.1339	3514	X-RAY DIFFRACTION	100
3.4547-4.3517	0.1576	210	0.1227	3497	X-RAY DIFFRACTION	100
4.3517-39.2268	0.1589	229	0.1457	3521	X-RAY DIFFRACTION	100

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	1.7696	0.1243	0.0014	1.0329	-0.7883	0.6164	0.034	-0.1001	0.0106	0.072	-0.0421	-0.0604	0.0209	0.0179	0.0364	0.0744	0.0104	-0.0017	0.0613	0.0104	0.1108	20.6476	58.1261	53.4696
2	0.7166	0.4069	-0.0551	2.6761	0.4397	0.7384	0.0274	0.0209	-0.1391	0.1045	-0.0228	0.0198	0.1343	0.0771	-0.0052	0.0947	0.0151	-0.0043	0.0831	0.011	0.1326	24.25	51.9779	47.8183
3	2.24	-0.0549	0.6312	1.5902	-0.1171	1.2419	-0.0077	-0.1327	-0.1558	0.1006	0.0198	0.0955	-0.01	-0.11	-0.0086	0.0915	0.0105	0.0043	0.0617	0.0091	0.0824	13.4085	57.2199	54.3856
4	1.1075	-0.2429	0.3263	0.562	0.0836	0.9544	-0.0099	-0.0628	0.0518	0.0308	-0.0159	-0.0361	-0.0492	-0.017	0.0293	0.0802	0.0021	0.0008	0.0617	0.0048	0.0993	9.7838	63.7315	53.7212
5	1.5993	0.4007	1.2836	2.3158	1.5434	3.8701	-0.1047	0.528	-0.0243	-0.419	0.1292	-0.1585	-0.1859	0.3053	-0.0777	0.1668	-0.0015	0.0062	0.2261	-0.0179	0.1269	5.8534	60.504	28.5905
6	2.2237	-0.4684	-0.2947	1.1038	0.0796	0.9801	0.0423	0.3767	0.0158	-0.1372	-0.0611	0.0785	-0.0278	-0.1316	0.0092	0.1209	0.0057	-0.0124	0.1626	-0.0034	0.1536	-5.3691	60.7406	35.1683
7	6.2288	0.8793	-0.3048	3.9979	-0.4798	6.9283	-0.0693	-0.0013	-0.6365	0.0029	-0.1454	0.056	0.5607	-0.0118	0.1868	0.1797	0.0251	0.0133	0.1235	-0.0086	0.2724	4.7129	48.8077	37.9792
8	1.5595	0.1078	0.8593	0.7006	0.3001	1.3999	-0.034	0.372	-0.0344	-0.1894	-0.0393	0.0295	-0.0556	0.1252	0.0738	0.129	0.0177	0.0028	0.1592	-0.0062	0.1178	8.4934	60.2482	34.5449
9	1.8709	0.168	-1.9045	1.0367	-0.4675	4.2061	0.0191	-0.1127	0.0205	0.1008	-0.0331	-0.1038	-0.157	0.0692	0.0256	0.1115	-0.0005	-0.0157	0.0838	0.0143	0.1183	23.6394	72.234	51.6828
10	5.5097	-1.4519	-0.8718	5.8819	-1.0407	3.6843	-0.1692	0.6905	0.0856	-0.2911	0.071	0.2339	0.1996	-0.1854	-0.0153	0.1059	-0.0253	0.0107	0.1784	0.0104	0.1227	25.1285	62.6179	36.0142
11	1.9004	0.0168	-0.7993	0.6448	0.672	2.1052	-0.0221	-0.1219	-0.085	0.094	0.0225	-0.0046	0.1083	-0.0754	0.0278	0.0713	0.0085	-0.0098	0.071	0.0122	0.0558	7.272	91.0861	53.5031
12	1.1395	0.0333	-0.3762	0.8589	-0.1656	1.6891	0.0229	0.0103	0.0522	0.034	-0.0146	0.0817	-0.088	-0.1341	-0.0146	0.0602	0.0156	-0.0009	0.073	-0.002	0.0694	2.7813	95.2103	48.819
13	4.0771	-0.5163	0.806	1.5535	0.0798	1.8795	0.0559	-0.1912	0.2276	-0.03	-0.007	-0.3132	-0.0895	0.2006	-0.0245	0.0703	-0.0132	0.0002	0.0873	-0.007	0.0926	25.9579	95.8753	50.966
14	1.0403	-0.1878	-0.6327	0.721	0.0396	0.9973	-0.0204	-0.069	-0.0735	0.0007	0.0103	0.0176	0.0428	0.0082	0.0028	0.0608	0.0018	-0.0104	0.0538	0.007	0.0569	18.7333	86.7087	51.1197
15	0.8264	-0.0956	0.0948	0.8108	-0.4506	2.1086	0.0461	0.1251	-0.0416	-0.0581	-0.0308	-0.087	0.0638	0.142	-0.0254	0.097	-0.0026	0.0039	0.1282	-0.0068	0.0626	32.6308	89.9605	24.4926
16	2.6595	-0.0593	-0.5915	1.1045	0.5328	1.4724	0.0024	-0.0743	-0.2	0.0503	0.001	-0.0848	0.0466	0.1462	-0.01	0.0786	0.0034	-0.0078	0.0929	0.0034	0.0754	32.986	87.1266	39.3688
17	6.0118	0.2118	-1.2955	5.2437	-0.6135	5.5576	0.0282	-0.0421	0.2798	0.1541	-0.0265	0.0176	-0.325	-0.0317	0.0066	0.1141	0.0116	0.0157	0.0698	-0.0072	0.0802	23.6465	100.5606	34.6839
18	1.1555	0.1458	-1.1515	0.3317	-0.2937	1.415	-0.0495	0.1366	-0.0613	-0.0836	-0.0046	-0.0225	0.1236	-0.0704	0.0428	0.0947	-0.0011	-0.0065	0.099	-0.0114	0.0731	18.5421	87.6743	36.6717
19	0.7853	-0.4442	1.665	1.2062	-0.8704	3.7857	0.0358	0.0443	-0.1218	0.0926	-0.0405	0.0799	0.0855	-0.0101	0.0255	0.0863	-0.002	0.004	0.0836	-0.0149	0.1212	2.7535	78.8907	46.2989
20	1.8505	-0.3701	-1.0132	1.6503	-0.2568	0.6896	-0.2274	0.8665	0.0464	-0.3572	0.001	-0.2221	-0.1877	0.0459	0.0788	0.1601	-0.0582	-0.0006	0.3603	0.0009	0.107	5.3282	89.1778	29.1609

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:20)
2	X-RAY DIFFRACTION	2	(chain A and resid 21:43)
3	X-RAY DIFFRACTION	3	(chain A and resid 44:72)
4	X-RAY DIFFRACTION	4	(chain A and resid 73:109)
5	X-RAY DIFFRACTION	5	(chain A and resid 110:121)
6	X-RAY DIFFRACTION	6	(chain A and resid 122:166)
7	X-RAY DIFFRACTION	7	(chain A and resid 167:177)
8	X-RAY DIFFRACTION	8	(chain A and resid 178:220)
9	X-RAY DIFFRACTION	9	(chain A and resid 221:240)
10	X-RAY DIFFRACTION	10	(chain A and resid 241:251)
11	X-RAY DIFFRACTION	11	(chain B and resid 1:21)
12	X-RAY DIFFRACTION	12	(chain B and resid 22:56)
13	X-RAY DIFFRACTION	13	(chain B and resid 57:72)
14	X-RAY DIFFRACTION	14	(chain B and resid 73:113)
15	X-RAY DIFFRACTION	15	(chain B and resid 114:139)
16	X-RAY DIFFRACTION	16	(chain B and resid 140:166)
17	X-RAY DIFFRACTION	17	(chain B and resid 167:177)
18	X-RAY DIFFRACTION	18	(chain B and resid 178:226)
19	X-RAY DIFFRACTION	19	(chain B and resid 227:244)
20	X-RAY DIFFRACTION	20	(chain B and resid 245:255)

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