PDB-8oon: Glutamine synthetase from Methanothermococcus thermolithotrophicu...

ID or keywords:

Entry

Database: PDB / ID: 8oon

Title

Glutamine synthetase from Methanothermococcus thermolithotrophicus at a resolution of 2.43 A

Components

Glutamine synthetase from Methanothermococcus thermolithotrophicus

Keywords

LIGASE / Nitrogen-assimilation / methanogenic archaea / allosteric activation / hydrogenotrophic / thermophile / marine / glutamate / ATP

Biological species

Methanothermococcus thermolithotrophicus DSM 2095 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.43 Å

Authors

Mueller, M.-C. / Lemaire, O.N. / Wagner, T.

Funding support

Germany, 2items

Citation

Journal: Commun Biol / Year: 2024
Title: Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations.
Authors: Muller, M.C. / Lemaire, O.N. / Kurth, J.M. / Welte, C.U. / Wagner, T.

History

Deposition	Apr 5, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 24, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	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 / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8oon.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8oon.ent.gz		Display	PDB format
PDBx/mmJSON format	8oon.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8oon_validation.pdf.gz	511.6 KB	Display	wwPDB validaton report
Full document	8oon_full_validation.pdf.gz	533.6 KB	Display
Data in XML	8oon_validation.xml.gz	91.6 KB	Display
Data in CIF	8oon_validation.cif.gz	124.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oo/8oon ftp://data.pdbj.org/pub/pdb/validation_reports/oo/8oon	HTTPS FTP

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Related structure data

Related structure data	8oolC 8oooC 8ooqC 8oowC 8ooxC 8oozC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glutamine synthetase from Methanothermococcus thermolithotrophicus

B: Glutamine synthetase from Methanothermococcus thermolithotrophicus

C: Glutamine synthetase from Methanothermococcus thermolithotrophicus

D: Glutamine synthetase from Methanothermococcus thermolithotrophicus

E: Glutamine synthetase from Methanothermococcus thermolithotrophicus

F: Glutamine synthetase from Methanothermococcus thermolithotrophicus

hetero molecules

304 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutamine synthetase from Methanothermococcus thermolithotrophicus

B: Glutamine synthetase from Methanothermococcus thermolithotrophicus

C: Glutamine synthetase from Methanothermococcus thermolithotrophicus

D: Glutamine synthetase from Methanothermococcus thermolithotrophicus

E: Glutamine synthetase from Methanothermococcus thermolithotrophicus

F: Glutamine synthetase from Methanothermococcus thermolithotrophicus

hetero molecules

A: Glutamine synthetase from Methanothermococcus thermolithotrophicus

B: Glutamine synthetase from Methanothermococcus thermolithotrophicus

C: Glutamine synthetase from Methanothermococcus thermolithotrophicus

D: Glutamine synthetase from Methanothermococcus thermolithotrophicus

E: Glutamine synthetase from Methanothermococcus thermolithotrophicus

F: Glutamine synthetase from Methanothermococcus thermolithotrophicus

hetero molecules

defined by author
Evidence: native gel electrophoresis, gel filtration
608 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	132.647, 230.244, 205.586
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Glutamine synthetase from Methanothermococcus thermolithotrophicus Mass: 50296.039 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Methanothermococcus thermolithotrophicus DSM 2095 (archaea) Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: DSM 2095 / Tissue: / / References: glutamine synthetase
#2: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.79 % / Description: Hexagonal plates
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Protein was crystallized fresh without any freezing step by using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI, United Kingdom) under ...Details: Protein was crystallized fresh without any freezing step by using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI, United Kingdom) under anaerobic conditions (N2:H2, gas ratio of 97:3). The enzyme was crystallized at 15 mg/ml in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 150 mM NaCl, and 2 mM dithiothreitol. The crystallization reservoir contained 90 uL of mother liquor (20 % w/v polyethylene glycol 3,350 and 100 mM potassium sodium tartrate), the crystallization drop contained a mixture of 0.55 uL protein and 0.55 uL mother liquor. Crystals were soaked in the mother liquor supplemented with 25% v/v ethylene glycol prior to freezing in liquid nitrogen.

Crystal

Density Matthews: 2.6 Å³/Da / Density % sol: 52.79 % / Description: Hexagonal plates

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Protein was crystallized fresh without any freezing step by using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI, United Kingdom) under ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00004 Å / Relative weight: 1
Reflection	Resolution: 2.43→76.675 Å / Num. obs: 102291 / % possible obs: 93.3 % / Redundancy: 14.5 % / B_iso Wilson estimate: 41.5 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.269 / R_pim(I) all: 0.073 / R_rim(I) all: 0.279 / Net I/σ(I): 7.4
Reflection shell	Resolution: 2.43→2.567 Å / Redundancy: 15.6 % / R_merge(I) obs: 1.795 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5117 / CC_1/2: 0.782 / R_pim(I) all: 0.464 / R_rim(I) all: 1.855 / % possible all: 49.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.43→58.89 Å / Cross valid method: FREE R-VALUE / σ(F): 205.88 / Phase error: 34.94 / Stereochemistry target values: TWIN_LSQ_F
Details: The structure was refined by applying translation libration screw model (TLS) and adding riding hydrogens. In addition, this dataset was refined by applying the following twin operator: ...

	R_factor	Num. reflection	% reflection
R_free	0.2682	7869	7.69 %
R_work	0.2294	-	-
obs	0.233	102286	86.6 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.65 Å²

Refinement step

Cycle: LAST / Resolution: 2.43→58.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21048	0	154	293	21495

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	21741
X-RAY DIFFRACTION	f_angle_d	0.654	29380
X-RAY DIFFRACTION	f_dihedral_angle_d	17.066	8083
X-RAY DIFFRACTION	f_chiral_restr	0.046	3143
X-RAY DIFFRACTION	f_plane_restr	0.004	3851

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 (%)
2.43-2.47	0.2989	28	0.2789	639	X-RAY DIFFRACTION	11
2.47-2.52	0.3385	78	0.2766	1468	X-RAY DIFFRACTION	25
2.52-2.56	0.3475	132	0.2845	2621	X-RAY DIFFRACTION	45
2.56-2.62	0.3189	174	0.2869	3696	X-RAY DIFFRACTION	63
2.62-2.67	0.3643	268	0.282	4644	X-RAY DIFFRACTION	79
2.67-2.74	0.3108	231	0.2884	5357	X-RAY DIFFRACTION	92
2.74-2.8	0.3437	274	0.2704	5591	X-RAY DIFFRACTION	95
2.8-2.88	0.3011	288	0.2623	5603	X-RAY DIFFRACTION	95
2.88-2.97	0.3033	324	0.2614	5501	X-RAY DIFFRACTION	94
2.97-3.06	0.3199	276	0.2593	5614	X-RAY DIFFRACTION	95
3.06-3.17	0.2697	318	0.2508	5549	X-RAY DIFFRACTION	95
3.17-3.3	0.2994	330	0.2478	5541	X-RAY DIFFRACTION	94
3.3-3.45	0.2906	243	0.2419	5675	X-RAY DIFFRACTION	96
3.45-3.63	0.2557	276	0.231	5600	X-RAY DIFFRACTION	95
3.63-3.86	0.2748	257	0.2229	5659	X-RAY DIFFRACTION	96
3.86-4.15	0.2971	241	0.2111	5712	X-RAY DIFFRACTION	96
4.15-4.57	0.2215	348	0.1936	5578	X-RAY DIFFRACTION	94
4.57-5.23	0.2299	273	0.1986	5672	X-RAY DIFFRACTION	95
5.23-6.59	0.284	289	0.2338	5728	X-RAY DIFFRACTION	95
6.59-58.89	0.2186	262	0.2082	5928	X-RAY DIFFRACTION	96

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	1.4328	0.7776	-0.0253	1.1271	-0.4503	1.2424	-0.1481	0.3849	-0.0932	-0.6569	0.0815	-0.3076	0.3833	0.3145	0.0078	0.5862	-0.0208	0.2117	0.4268	-0.0754	0.4019	12.6491	-18.5864	16.29
2	2.0804	-0.155	-0.0744	2.091	-0.6877	1.5495	0.0147	0.1582	0.1313	-0.2767	0.0469	0.0749	-0.1401	-0.1947	-0.1453	0.2511	-0.0654	0.1413	0.2663	-0.0009	0.3961	-7.1543	-9.9151	27.1667
3	1.4269	0.8394	0.7229	1.842	-0.539	1.0674	0.1351	0.015	-0.2194	-0.0371	-0.0102	0.1914	0.886	-0.5444	-0.0515	0.7882	-0.213	0.1527	0.3756	-0.0439	0.4904	-10.8996	-34.2959	29.4593
4	0.8738	0.3198	-0.0282	1.525	0.6496	2.2773	0.0055	-0.0266	-0.1793	-0.3754	0.1295	-0.137	0.224	0.1743	-0.0747	0.4883	-0.0698	0.1555	0.2397	0.0019	0.3511	4.3236	-27.568	44.4526
5	1.8986	-0.1767	-0.9483	0.7456	0.241	1.9922	0.0516	0.4344	-0.3165	-0.4703	-0.1494	0.0959	0.4466	-0.0903	0.1731	0.7731	-0.0442	0.0952	0.416	-0.0548	0.3744	-22.1258	-12.607	13.7935
6	1.632	0.1193	-0.457	1.4298	-0.0262	1.3191	-0.0219	0.2207	-0.186	-0.0464	-0.0316	-0.1793	0.3165	-0.249	-0.0204	0.5068	-0.0548	0.1071	0.3196	0.0014	0.2932	-32.1202	-0.381	22.7022
7	1.2883	0.4505	0.255	1.4726	0.4789	1.6314	0.1162	0.3329	0.1509	-0.0677	-0.0698	0.0926	0.3116	-0.3321	-0.0334	0.3951	-0.011	0.1304	0.3753	0.0273	0.3163	-38.5607	7.9292	22.6718
8	1.7387	-0.0447	0.6587	1.2472	-0.1655	2.4657	-0.1463	-0.1415	0.3656	0.0876	0.0071	0.418	-0.0303	-0.9921	0.1579	0.3644	-0.0394	0.1272	0.6454	-0.0399	0.4956	-52.6321	3.035	32.0908
9	1.2833	0.1861	0.6913	0.7431	0.4203	2.4094	0.0047	-0.0196	-0.2363	0.1677	0.0802	0.108	0.4744	-0.4003	-0.0038	0.5581	-0.0663	0.1591	0.3712	0.0372	0.2879	-40.6759	-6.3996	44.3942
10	1.2507	-0.4151	0.4421	1.6382	0.437	0.6672	-0.0175	0.466	-0.0939	-0.7774	-0.0236	0.2359	0.1785	-0.109	0.0415	0.5337	-0.0346	0.1423	0.4514	-0.0016	0.3613	-36.584	25.3729	12.3188
11	2.3418	-0.2509	0.039	2.2535	0.0335	3.0619	0.0277	0.2203	-0.2155	-0.3585	-0.1043	0.1917	0.3334	-0.4451	0.0723	0.3697	0.0084	0.0789	0.4017	-0.0414	0.3956	-42.984	25.8219	15.7141
12	2.8002	0.2082	0.3162	0.7167	0.3167	1.989	-0.0157	0.2115	0.0627	-0.1507	-0.0041	-0.0979	-0.1125	0.1193	-0.0571	0.2271	0.0298	0.1604	0.2454	0.0275	0.4278	-29.1369	44.291	25.4897
13	2.005	-0.2429	0.2311	0.5212	0.1133	1.6973	0.1539	0.1178	0.1506	-0.2819	-0.0716	-0.0106	-0.5867	-0.2152	-0.0733	0.4165	0.1024	0.164	0.326	0.0446	0.4015	-35.6319	49.962	25.7696
14	2.5286	-1.4304	1.5059	2.5109	-1.5633	5.0706	-0.1449	0.1731	0.5631	0.0993	-0.2262	-0.4292	-1.4215	0.2501	-0.1938	0.5264	0.0586	0.2482	0.3579	0.0337	0.5642	-37.45	58.805	30.3461
15	2.0558	-1.206	-0.0383	2.7437	-0.4945	1.388	-0.0341	-0.1152	0.3978	0.4706	-0.0249	0.1463	-1.1018	-0.43	-0.0402	0.8816	0.186	0.1748	0.512	0.0949	0.4306	-46.0133	60.5516	33.4842
16	0.2249	-0.0373	-0.1383	0.1465	0.1679	0.2495	0.0721	0.0605	0.1228	0.0701	-0.0942	0.4595	-0.0639	-0.3934	0.0732	-0.6213	0.1712	0.4267	0.463	0.06	0.4596	-44.5158	42.222	44.4753
17	1.6307	0.2658	0.3029	1.0341	0.1417	0.809	-0.1136	0.2785	0.0273	-0.1298	0.1271	0.0558	-0.2696	-0.076	-0.0268	0.6682	0.0373	0.1565	0.3248	0.0382	0.2652	-4.2953	58.0018	20.6362
18	0.8772	0.4973	-0.5253	1.7301	-1.5132	3.2869	-0.0742	0.0622	0.247	0.0734	-0.0389	-0.2298	-0.6514	0.5018	0.0917	0.6063	-0.0943	0.1535	0.3055	0.0157	0.4589	6.3376	75.184	34.0181
19	1.2969	0.0706	0.0397	0.7194	-0.3136	1.0402	-0.01	0.325	0.1321	-0.3675	-0.003	-0.0721	-0.1473	0.1133	-0.0134	0.5237	-0.0261	0.1816	0.3417	-0.0066	0.3076	29.3444	43.4808	20.7249
20	1.1339	0.4556	-0.8234	0.5545	-0.0157	2.5397	-0.1372	-0.0056	0.1135	-0.0984	0.1421	-0.3258	0.3458	0.6747	0.0657	0.3034	-0.0449	0.1853	0.5216	-0.0182	0.5042	49.5421	42.7446	34.0259
21	1.1085	-0.2263	0.1683	1.3255	0.0069	0.5996	-0.0282	0.1077	-0	-0.1647	0.0075	-0.0462	0.0259	0.1992	0.0216	0.4423	-0.0131	0.147	0.3514	-0.0377	0.2876	33.6661	7.1306	20.8154
22	0.7586	-0.2743	-0.1064	0.9096	0.9464	2.0163	-0.0831	0.0071	-0.325	0.1743	0.0984	-0.1134	0.6009	0.3878	-0.0381	0.5914	0.182	0.1503	0.3592	-0.0025	0.4199	43.2348	-10.6574	33.9764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 145 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 146 through 248 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 249 through 388 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 389 through 448 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 71 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 72 through 170 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 171 through 273 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 274 through 387 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 388 through 448 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 39 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 40 through 112 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 113 through 182 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 183 through 303 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 304 through 347 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 348 through 388 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 389 through 448 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 248 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 249 through 448 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 248 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 249 through 448 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 2 through 248 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 249 through 448 )

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