PDB-4ykk: Mnemiopsis leidyi ML032222a iGluR LBD D-serine complex

ID or keywords:

Entry

Database: PDB / ID: 4ykk

Title

Mnemiopsis leidyi ML032222a iGluR LBD D-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: 1.38 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ykk.cif.gz	323.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ykk.ent.gz	268 KB	Display	PDB format
PDBx/mmJSON format	4ykk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ykk_validation.pdf.gz	467.6 KB	Display	wwPDB validaton report
Full document	4ykk_full_validation.pdf.gz	470.7 KB	Display
Data in XML	4ykk_validation.xml.gz	28.5 KB	Display
Data in CIF	4ykk_validation.cif.gz	45.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yk/4ykk ftp://data.pdbj.org/pub/pdb/validation_reports/yk/4ykk	HTTPS FTP

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Related structure data

Related structure data	4ykiSC 4ykjC 4ykpC 4zdmC 4ykv PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cmb-d 4ykp-d 4ykj-d 3g3g-d 4io5-d 4yki-d 5fth-1 4bdn-2 4bdm-1 3g3j-d 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)	45.951, 123.753, 54.505
Angle α, β, γ (deg.)	90.00, 111.78, 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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-DSN / D-SERINE Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H₂O
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 D-Serine, no added glycine

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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: 1.38→40 Å / Num. obs: 115480 / % possible obs: 99.6 % / Redundancy: 3.7 % / R_merge(I) obs: 0.065 / Net I/σ(I): 19.5
Reflection shell	Resolution: 1.38→1.4 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.61 / Mean I/σ(I) obs: 1.7 / % possible all: 95.6

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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: 1.38→35.128 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1672	5807	5.05 %	Random
R_work	0.1437	-	-	-
obs	0.1449	114973	99.4 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.38→35.128 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4010	0	25	778	4813

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4319
X-RAY DIFFRACTION	f_angle_d	1.233	5844
X-RAY DIFFRACTION	f_dihedral_angle_d	13.002	1602
X-RAY DIFFRACTION	f_chiral_restr	0.074	619
X-RAY DIFFRACTION	f_plane_restr	0.006	773

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 (%)
1.38-1.3957	0.2834	177	0.2564	3285	X-RAY DIFFRACTION	89
1.3957-1.4121	0.253	181	0.2342	3513	X-RAY DIFFRACTION	97
1.4121-1.4293	0.2382	191	0.2206	3596	X-RAY DIFFRACTION	98
1.4293-1.4474	0.2495	197	0.2139	3619	X-RAY DIFFRACTION	99
1.4474-1.4665	0.2167	187	0.2007	3658	X-RAY DIFFRACTION	100
1.4665-1.4866	0.2201	199	0.185	3654	X-RAY DIFFRACTION	100
1.4866-1.5078	0.2062	189	0.1773	3603	X-RAY DIFFRACTION	100
1.5078-1.5303	0.2022	195	0.1726	3688	X-RAY DIFFRACTION	100
1.5303-1.5542	0.1948	196	0.1672	3651	X-RAY DIFFRACTION	100
1.5542-1.5797	0.1826	201	0.1628	3618	X-RAY DIFFRACTION	100
1.5797-1.6069	0.1789	199	0.1627	3660	X-RAY DIFFRACTION	100
1.6069-1.6362	0.1762	186	0.1497	3653	X-RAY DIFFRACTION	100
1.6362-1.6676	0.1712	194	0.1462	3679	X-RAY DIFFRACTION	100
1.6676-1.7017	0.1776	194	0.1464	3663	X-RAY DIFFRACTION	100
1.7017-1.7387	0.1778	199	0.147	3619	X-RAY DIFFRACTION	100
1.7387-1.7791	0.1743	186	0.1424	3677	X-RAY DIFFRACTION	100
1.7791-1.8236	0.1703	205	0.1401	3653	X-RAY DIFFRACTION	100
1.8236-1.8729	0.1509	187	0.1417	3650	X-RAY DIFFRACTION	100
1.8729-1.928	0.1379	201	0.1375	3660	X-RAY DIFFRACTION	100
1.928-1.9902	0.1653	179	0.1326	3681	X-RAY DIFFRACTION	100
1.9902-2.0614	0.1525	206	0.1328	3618	X-RAY DIFFRACTION	100
2.0614-2.1439	0.1512	183	0.1269	3665	X-RAY DIFFRACTION	100
2.1439-2.2414	0.1382	191	0.1275	3676	X-RAY DIFFRACTION	100
2.2414-2.3596	0.1631	180	0.1306	3693	X-RAY DIFFRACTION	100
2.3596-2.5074	0.17	178	0.134	3686	X-RAY DIFFRACTION	100
2.5074-2.7009	0.1792	193	0.1357	3690	X-RAY DIFFRACTION	100
2.7009-2.9726	0.1492	189	0.1437	3637	X-RAY DIFFRACTION	100
2.9726-3.4024	0.1556	189	0.1343	3692	X-RAY DIFFRACTION	100
3.4024-4.2855	0.1579	212	0.1244	3661	X-RAY DIFFRACTION	100
4.2855-35.1389	0.1559	243	0.1396	3668	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	3.2346	-0.1528	3.3884	8.5904	-0.576	3.6784	0.0285	-0.5099	0.3561	0.7676	0.0177	0.3633	-0.5057	-0.1245	-0.0927	0.2646	-0.0274	-0.0407	0.2605	-0.0239	0.2968	27.3366	65.6716	64.5955
2	1.1468	0.0455	0.0167	0.765	0.3152	0.8966	0.0188	0.0213	-0.1511	0.0237	-0.0208	-0.0434	0.1407	0.0752	-0.0022	0.1078	0.017	-0.0007	0.0835	0.0056	0.1418	21.8375	53.5305	48.5101
3	2.7965	0.1261	0.6222	1.7142	-0.134	1.1869	0.0143	-0.1549	-0.08	0.1075	-0.0083	0.068	0.014	-0.0859	-0.0044	0.11	0.008	0.0042	0.0753	0.0012	0.101	14.0583	57.5152	54.6094
4	1.293	-0.0087	0.3668	0.6629	0.0364	1.091	-0.0227	0.0604	0.0198	-0.0428	-0.0174	-0.0115	-0.0085	-0.0023	0.0312	0.0939	0.0008	0.0072	0.0661	0.0018	0.1205	8.8344	63.2582	48.5558
5	2.1682	-0.385	-0.2239	1.2995	0.0744	1.3254	0.0065	0.5035	0.0067	-0.1098	-0.0533	0.0789	-0.0537	-0.1518	0.0155	0.1157	-0.0043	-0.0108	0.2068	-0.0232	0.1691	-5.6864	60.8512	35.1539
6	8.8604	1.5867	-0.6154	5.4548	-1.4397	8.2885	-0.0506	0.0804	-0.7004	0.0612	-0.0791	-0.0654	0.6386	-0.0003	0.1407	0.2294	0.0374	0.0546	0.1523	-0.0064	0.3795	4.5161	48.8443	38.3
7	1.84	0.2291	0.8484	0.8224	0.5404	1.567	-0.0809	0.5106	-0.069	-0.2135	-0.0335	0.0436	-0.0286	0.1756	0.0955	0.1547	0.0135	0.0013	0.2068	-0.0239	0.1441	8.0289	60.0109	34.5078
8	1.9474	0.28	-1.7915	1.246	-0.2527	4.6316	0.0667	-0.1079	0.0544	0.1041	-0.0152	-0.1164	-0.1157	0.0267	-0.0306	0.1175	-0.0019	-0.0147	0.0963	0.0169	0.1294	23.4175	72.124	52.473
9	5.366	-0.5768	0.1464	5.8086	0.1568	3.2387	-0.2358	0.6122	-0.009	-0.2796	0.0196	0.2547	0.0958	-0.1541	0.1027	0.1309	-0.0256	0.0155	0.2076	-0.0037	0.1711	24.7117	62.8463	36.7129
10	2.1433	0.137	-0.6052	0.7176	0.7874	2.053	-0.0067	-0.1658	-0.0985	0.1187	0.003	0.0399	0.1233	-0.0179	0.0567	0.0823	0.0174	-0.0062	0.0607	0.0153	0.0674	7.1619	90.8276	54.217
11	1.1659	-0.0894	-0.4321	0.985	-0.1834	1.8288	0.0172	0.0257	0.056	0.0354	-0.0051	0.0756	-0.097	-0.1524	-0.0201	0.0709	0.0161	-0.0001	0.0875	0.0002	0.0796	2.7016	95.07	48.5642
12	3.9121	-0.1767	0.1784	1.5759	0.0345	1.7469	0.0571	-0.1443	0.2838	-0.0081	-0.0587	-0.3136	-0.1273	0.2475	0.0148	0.0918	-0.0175	-0.0064	0.1138	-0.0008	0.1175	25.1435	96.0789	51.304
13	0.7259	0.1027	-0.6502	0.1436	-0.2082	1.0319	-0.0331	-0.0005	-0.0546	-0.0357	0.0034	-0.0021	0.0447	-0.018	0.0207	0.0734	0.001	-0.0081	0.0535	-0.0007	0.0665	19.7671	87.2711	46.6618
14	1.6229	0.0389	0.0056	0.7115	-0.392	2.0072	-0.0079	0.02	-0.1422	-0.0004	-0.0319	-0.0564	0.0613	0.2187	0.0153	0.0813	-0.0054	0.0015	0.1036	-0.0061	0.0847	33.8956	88.1486	33.9687
15	5.8574	-1.0185	-1.5918	5.1906	-1.2141	6.6177	0.0614	-0.0995	0.4107	0.0991	-0.1054	-0.0079	-0.4715	-0.0935	0.0914	0.1433	0.0179	0.009	0.0955	-0.0317	0.126	23.8087	100.7976	34.582
16	1.212	0.148	-1.1661	0.3813	-0.2383	1.1792	-0.0388	0.2436	-0.0685	-0.1119	0.0071	-0.0321	0.0863	-0.1719	0.034	0.1096	0.0005	-0.0013	0.1314	-0.0087	0.0713	19.9031	88.8161	32.9409
17	1.2246	-0.0726	1.069	0.696	0.0901	3.3848	0.0362	0.0361	-0.1692	0.0513	-0.0231	0.0978	0.2186	-0.0149	-0.0353	0.0969	-0.002	0.0117	0.0932	-0.0101	0.1346	4.4219	79.2923	50.1082
18	2.8674	-1.082	-2.2677	1.7643	-0.0117	2.3474	-0.2473	1.0172	0.0263	-0.3638	0.0738	-0.1272	-0.1851	0.0159	0.0104	0.1707	-0.0731	-0.0122	0.4446	-0.0197	0.1191	5.3426	89.1392	29.3569

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 4:8)
2	X-RAY DIFFRACTION	2	(chain A and resid 9:43)
3	X-RAY DIFFRACTION	3	(chain A and resid 44:72)
4	X-RAY DIFFRACTION	4	(chain A and resid 73:121)
5	X-RAY DIFFRACTION	5	(chain A and resid 122:166)
6	X-RAY DIFFRACTION	6	(chain A and resid 167:176)
7	X-RAY DIFFRACTION	7	(chain A and resid 177:220)
8	X-RAY DIFFRACTION	8	(chain A and resid 221:240)
9	X-RAY DIFFRACTION	9	(chain A and resid 241:250)
10	X-RAY DIFFRACTION	10	(chain B and resid 1:20)
11	X-RAY DIFFRACTION	11	(chain B and resid 21:55)
12	X-RAY DIFFRACTION	12	(chain B and resid 56:72)
13	X-RAY DIFFRACTION	13	(chain B and resid 73:122)
14	X-RAY DIFFRACTION	14	(chain B and resid 123:166)
15	X-RAY DIFFRACTION	15	(chain B and resid 167:177)
16	X-RAY DIFFRACTION	16	(chain B and resid 178:220)
17	X-RAY DIFFRACTION	17	(chain B and resid 221:244)
18	X-RAY DIFFRACTION	18	(chain B and resid 245:255)

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