PDB-4bax: Crystal structure of glutamine synthetase from Streptomyces coelicolor

ID or keywords:

Entry

Database: PDB / ID: 4bax

Title

Crystal structure of glutamine synthetase from Streptomyces coelicolor

Components

GLUTAMINE SYNTHETASE

Keywords

LIGASE

Function / homology

Function and homology information

glutamine synthetase / : / glutamine synthetase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

STREPTOMYCES COELICOLOR (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Zeth, K.

Citation

Journal: To be Published
Title: Structure of Glutamine Synthetase from Streptomyces Coelicolor
Authors: Zeth, K.

History

Deposition	Sep 16, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4bax.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4bax.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4bax.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/ba/4bax ftp://data.pdbj.org/pub/pdb/validation_reports/ba/4bax	HTTPS FTP

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Related structure data

Similar structure data	2d3c-d 2uu7-2 3fky-2 3fky-1 2d3a-d 2qc8-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	#30 - Jun 2002 Glutamine Synthetase similarity (12)

Deposited unit

A: GLUTAMINE SYNTHETASE

B: GLUTAMINE SYNTHETASE

C: GLUTAMINE SYNTHETASE

D: GLUTAMINE SYNTHETASE

E: GLUTAMINE SYNTHETASE

F: GLUTAMINE SYNTHETASE

G: GLUTAMINE SYNTHETASE

H: GLUTAMINE SYNTHETASE

I: GLUTAMINE SYNTHETASE

J: GLUTAMINE SYNTHETASE

hetero molecules

374 kDa, 10 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)	97.120, 113.000, 194.440
Angle α, β, γ (deg.)	90.00, 98.55, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	GLUTAMINE SYNTHETASE Mass: 37364.660 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9X958, glutamine synthetase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1076 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.44 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.55→25 Å / Num. obs: 134887 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / R_merge(I) obs: 0.09 / Net I/σ(I): 12

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→24.996 Å / SU ML: 0.34 / σ(F): 1.36 / Phase error: 22.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2358	6741	5 %
R_work	0.206	-	-
obs	0.2076	134887	99.64 %

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 24.738 Å² / k_sol: 0.339 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.7082 Å²	0 Å²	-1.3655 Å²
2-	-	3.2116 Å²	0 Å²
3-	-	-	1.4966 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→24.996 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26270	0	8	1076	27354

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	26940
X-RAY DIFFRACTION	f_angle_d	1.321	36670
X-RAY DIFFRACTION	f_dihedral_angle_d	15.482	9700
X-RAY DIFFRACTION	f_chiral_restr	0.089	3920
X-RAY DIFFRACTION	f_plane_restr	0.009	4870

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 (%)
2.55-2.5789	0.3481	223	0.3327	4245	X-RAY DIFFRACTION	100
2.5789-2.6093	0.346	226	0.3048	4284	X-RAY DIFFRACTION	100
2.6093-2.641	0.324	223	0.2973	4240	X-RAY DIFFRACTION	100
2.641-2.6744	0.3419	225	0.2958	4271	X-RAY DIFFRACTION	100
2.6744-2.7096	0.304	226	0.2836	4301	X-RAY DIFFRACTION	100
2.7096-2.7467	0.3069	221	0.2753	4197	X-RAY DIFFRACTION	100
2.7467-2.7859	0.2995	225	0.2748	4283	X-RAY DIFFRACTION	100
2.7859-2.8274	0.3098	223	0.2625	4238	X-RAY DIFFRACTION	100
2.8274-2.8715	0.2795	226	0.2509	4294	X-RAY DIFFRACTION	100
2.8715-2.9185	0.2864	226	0.2455	4289	X-RAY DIFFRACTION	100
2.9185-2.9688	0.2531	222	0.2342	4215	X-RAY DIFFRACTION	100
2.9688-3.0226	0.2826	225	0.242	4275	X-RAY DIFFRACTION	100
3.0226-3.0807	0.2776	224	0.2435	4254	X-RAY DIFFRACTION	100
3.0807-3.1434	0.2716	226	0.2325	4306	X-RAY DIFFRACTION	100
3.1434-3.2117	0.2604	224	0.2259	4251	X-RAY DIFFRACTION	100
3.2117-3.2862	0.2496	225	0.2174	4278	X-RAY DIFFRACTION	100
3.2862-3.3682	0.2355	224	0.2109	4256	X-RAY DIFFRACTION	100
3.3682-3.459	0.2516	228	0.2056	4330	X-RAY DIFFRACTION	100
3.459-3.5606	0.2631	223	0.2122	4232	X-RAY DIFFRACTION	100
3.5606-3.6751	0.2575	224	0.2069	4251	X-RAY DIFFRACTION	100
3.6751-3.8061	0.2324	225	0.1967	4279	X-RAY DIFFRACTION	100
3.8061-3.9579	0.2013	225	0.181	4282	X-RAY DIFFRACTION	100
3.9579-4.1372	0.1704	224	0.16	4256	X-RAY DIFFRACTION	99
4.1372-4.3543	0.1713	225	0.1506	4281	X-RAY DIFFRACTION	99
4.3543-4.6255	0.1695	224	0.1493	4254	X-RAY DIFFRACTION	99
4.6255-4.98	0.1717	224	0.1586	4256	X-RAY DIFFRACTION	99
4.98-5.4764	0.1946	224	0.1724	4271	X-RAY DIFFRACTION	99
5.4764-6.258	0.2188	224	0.1971	4283	X-RAY DIFFRACTION	99
6.258-7.8438	0.2199	227	0.1891	4308	X-RAY DIFFRACTION	99
7.8438-24.9969	0.1974	230	0.1655	4386	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	0.0239	0.012	-0.0141	0.0698	-0.0143	0.0216	-0.0003	0.0722	0.1214	-0.0825	0.0817	0.0803	0.1558	0.0428	0.0378	0.2003	-0.0001	-0.0154	0.2116	0.0448	0.1255	4.5831	-21.3079	16.0131
2	0.1525	0.0496	-0.0272	0.1585	-0.0726	0.226	-0.014	0.0008	0.041	-0.0648	-0.0358	0.1147	0.0553	0.007	-0.1841	0.1521	0.005	-0.0498	0.1315	-0.0333	0.1552	3.9384	-31.5459	33.8215
3	0.0501	-0.0064	-0.0266	0.072	0.0017	0.0432	-0.0513	0.0516	0.0014	0.1195	-0.0263	0.0024	0.082	-0.0484	-0.009	0.3231	-0.0273	-0.016	0.2203	-0.0089	0.214	0.7774	-46.8136	37.8226
4	0.0393	0.0476	-0.0443	0.1135	-0.0563	0.1331	-0.0314	-0.0168	0.0427	-0.0801	-0.0495	-0.1349	-0.0438	0.0339	-0.0941	0.3482	0.0322	-0.0648	0.2069	0.0118	0.288	13.3806	17.6431	13.9296
5	0.2494	0.0644	0.0302	0.4675	-0.0636	0.2993	-0.1088	0.0909	-0.0346	-0.1212	-0.0259	0.0138	0.0718	0.026	-0.2844	0.1269	0.0257	-0.0638	0.0952	0.0146	0.0833	14.4532	-2.5707	10.4232
6	0.1661	0.0062	-0.086	0.0217	-0.0108	0.0491	-0.0252	0.1553	-0.1284	-0.1646	-0.0467	0.1444	-0.0231	0.0049	-0.0325	0.4294	0.0069	-0.0658	0.2564	-0.0176	0.2517	16.0384	-11.4581	-2.8901
7	0.0309	0.0048	-0.0288	0.0438	-0.0183	0.0503	-0.0382	-0.1159	0.0745	0.0448	0.0476	0.0911	-0.1068	-0.1475	0.022	0.2635	0.0507	0.0393	0.3369	-0.0137	0.3275	10.0461	32.7476	50.9021
8	0.1579	-0.1277	0.0376	0.1219	0.0571	0.4063	-0.0103	0.0002	-0.0525	0.0082	0.0469	0.0669	0.042	0.0183	0.2501	0.1481	0.0147	0.0173	0.1669	0.0122	0.1981	17.3174	29.3321	32.0358
9	0.0881	0.0066	-0.0481	0.0393	-0.0176	0.0444	-0.1102	0.0319	0.0418	-0.078	0.0476	-0.0424	0.0539	0.0768	-0.0068	0.2511	0.0207	0.0006	0.2476	0.0303	0.2193	22.4273	38.9652	20.2034
10	0.0329	0.0341	-0.0453	0.0592	-0.0381	0.0603	-0.0314	-0.0774	-0.0542	0.1514	-0.0175	0.1439	0.0425	0.0268	-0.0201	0.2326	-0.0191	0.0611	0.3186	0.0198	0.3378	-0.3471	3.2663	75.8544
11	0.1996	0.0763	-0.1017	0.2281	-0.1761	0.149	0.0193	-0.0485	0.0624	0.1032	0.0107	0.0601	-0.0858	0.0424	0.1472	0.1029	-0.0083	0.0257	0.1056	-0.03	0.0843	9.0646	20.0391	68.6091
12	0.0326	-0.0045	0.0293	0.0524	-0.0175	0.032	0.0219	0.0115	0.2204	0.1331	0.0027	0.0593	-0.1048	0.0231	-0.0145	0.3907	-0.0268	0.0732	0.2896	-0.0651	0.2551	11.9505	34.6889	74.7825
13	0.0438	0.0231	0.0168	0.0562	0.0376	0.0445	-0.0526	0.0912	-0.0044	0.0748	-0.0116	0.0319	0.0485	-0.085	-0.1407	0.0329	0.0183	-0.1644	0.2557	-0.1373	0.2358	-3.9243	-30.0746	54.2208
14	0.2562	0.048	0.1341	0.4353	0.0836	0.3058	-0.0462	-0.1153	-0.0705	0.1376	0.0287	0.1022	-0.031	-0.1121	-0.1772	0.0955	-0.0093	0.0072	0.1607	0.0057	0.1437	0.9098	-17.7602	69.8346
15	0.0287	-0.0127	-0.0023	0.066	-0.0489	0.0898	-0.0366	-0.1109	-0.0466	0.1447	-0.0825	0.0259	0.0542	-0.1315	-0.0077	0.2463	-0.0097	0.0216	0.3686	0.0124	0.2515	-0.9369	-18.7618	85.8137
16	0.0477	0.0036	-0.0471	0.0059	0.0164	0.0837	0.011	0.0076	0.0562	0.0118	-0.0746	-0.0728	-0.0549	0.0742	-0.0821	0.1161	-0.0459	-0.0206	0.2612	0.0543	0.2574	61.7391	19.6255	65.2018
17	0.2103	0.1637	-0.0222	0.2363	-0.0422	0.0556	0.0495	-0.2838	-0.1917	0.309	-0.1898	-0.0158	0.0283	0.1232	-0.4055	-0.1484	-0.1057	-0.4008	0.1969	0.0184	-0.2809	52.0333	7.1644	78.3104
18	0.0609	-0.0219	0.0145	0.056	0.0165	0.0144	0.0102	-0.1701	-0.0135	0.3031	-0.2232	-0.1671	0.0534	0.1349	-0.0926	0.4707	-0.1341	-0.0271	0.5091	0.0269	0.3153	48.3746	8.0868	94.0066
19	0.0391	0.0078	-0.0106	0.1052	0.0617	0.0526	-0.0305	0.0594	-0.1338	-0.0457	0.0905	-0.2232	0.0117	0.0423	0.0983	0.3172	0.0371	0.1079	0.3909	-0.0258	0.4061	66.5411	10.927	26.618
20	0.183	-0.0507	-0.0324	0.2223	0.0311	0.1219	0.0157	0.0013	-0.0099	-0.0805	-0.0493	-0.1987	0.0028	0.0799	-0.0037	0.1536	0.0199	0.0561	0.2022	0.0252	0.2735	61.1268	21.2196	43.4922
21	0.0191	-0.0003	0.0143	0.0638	-0.0056	0.0197	0.052	0.0464	-0.0076	0.0226	-0.0015	-0.2718	0.027	0.1308	0.0046	0.2372	0.0043	0.018	0.2806	0.004	0.2935	62.6944	36.5667	48.1526
22	0	-0.0087	-0.0058	0.0295	-0.0132	0.1633	-0.0546	0.0145	-0.0923	-0.1928	-0.0271	-0.1121	-0.0252	-0.0052	-0.0642	0.4074	0.0502	0.1168	0.2714	0.0591	0.4057	58.9514	-27.9704	21.4329
23	0.1086	0.041	-0.0513	0.2348	0.1195	0.1326	0.0266	0.003	0.0053	-0.3232	-0.06	-0.1278	-0.0354	-0.0063	-0.3776	0.3457	0.0871	0.1107	0.1824	0.0253	0.2212	59.2107	-7.7062	17.9433
24	0.0254	0.0387	0.0043	0.06	0.0081	0.0558	0.0257	0.0258	-0.0182	-0.1788	-0.0296	-0.0974	-0.0555	-0.0552	-0.1139	0.6349	0.2496	0.4231	0.0439	-0.1594	0.1313	62.358	1.2331	4.9669
25	0.0714	-0.0062	0.0163	0.0385	0.014	0.1876	-0.0246	-0.0769	-0.0708	0.0527	0.0034	0.0026	0.1273	0.0602	0.0553	0.2337	0.0173	0.0662	0.3429	0.0646	0.2533	50.1058	-43.2286	57.2295
26	0.0962	0.038	-0.1123	0.2229	-0.0046	0.1804	-0.0329	-0.0142	-0.0623	-0.0612	0.0522	0.0093	-0.0653	-0.0175	0.0283	0.1363	0.0307	0.0244	0.1084	0.0299	0.1703	49.3475	-39.7274	37.0098
27	0.0576	-0.0086	0.0276	0.0315	0.0001	0.0493	-0.148	-0.0597	0.0309	-0.0633	-0.0037	-0.0392	0.0193	0.0324	-0.0083	0.3263	0.0158	0.0288	0.1646	0.0048	0.3201	48.4664	-49.2194	24.0562
28	0.0522	0.0129	-0.0611	0.0822	0.006	0.1178	-0.0508	-0.0353	-0.047	0.0822	-0.0056	0.0638	-0.0426	-0.079	-0.0854	0.2677	-0.029	-0.0983	0.3708	0.0796	0.3189	51.1779	-13.9209	84.3186
29	0.1926	-0.0665	0.1341	0.3365	0.1511	0.3712	-0.0646	-0.0326	-0.0571	0.057	-0.0819	-0.1653	0.1231	-0.0548	-0.6533	0.2017	-0.0212	-0.0113	0.2549	0.0673	0.2143	45.0275	-30.6825	74.3379
30	0.0666	-0.0215	-0.0157	0.0176	-0.0036	0.0268	-0.0569	-0.1248	-0.0655	0.0619	-0.0347	-0.1739	0.1805	0.0105	-0.019	0.4324	-0.0715	-0.0131	0.2615	0.0606	0.2076	40.5662	-45.4438	78.9723

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 6:60)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 61:279)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 280:349)
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESSEQ 6:60)
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 61:279)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 280:349)
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESSEQ 6:60)
8	X-RAY DIFFRACTION	8	CHAIN C AND (RESSEQ 61:279)
9	X-RAY DIFFRACTION	9	CHAIN C AND (RESSEQ 280:349)
10	X-RAY DIFFRACTION	10	CHAIN D AND (RESSEQ 6:60)
11	X-RAY DIFFRACTION	11	CHAIN D AND (RESSEQ 61:279)
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESSEQ 280:349)
13	X-RAY DIFFRACTION	13	CHAIN E AND (RESSEQ 6:60)
14	X-RAY DIFFRACTION	14	CHAIN E AND (RESSEQ 61:279)
15	X-RAY DIFFRACTION	15	CHAIN E AND (RESSEQ 280:349)
16	X-RAY DIFFRACTION	16	CHAIN F AND (RESSEQ 6:60)
17	X-RAY DIFFRACTION	17	CHAIN F AND (RESSEQ 61:279)
18	X-RAY DIFFRACTION	18	CHAIN F AND (RESSEQ 280:349)
19	X-RAY DIFFRACTION	19	CHAIN G AND (RESSEQ 6:60)
20	X-RAY DIFFRACTION	20	CHAIN G AND (RESSEQ 61:279)
21	X-RAY DIFFRACTION	21	CHAIN G AND (RESSEQ 280:349)
22	X-RAY DIFFRACTION	22	CHAIN H AND (RESSEQ 6:60)
23	X-RAY DIFFRACTION	23	CHAIN H AND (RESSEQ 61:279)
24	X-RAY DIFFRACTION	24	CHAIN H AND (RESSEQ 280:349)
25	X-RAY DIFFRACTION	25	CHAIN I AND (RESSEQ 6:60)
26	X-RAY DIFFRACTION	26	CHAIN I AND (RESSEQ 61:279)
27	X-RAY DIFFRACTION	27	CHAIN I AND (RESSEQ 280:349)
28	X-RAY DIFFRACTION	28	CHAIN J AND (RESSEQ 6:60)
29	X-RAY DIFFRACTION	29	CHAIN J AND (RESSEQ 61:279)
30	X-RAY DIFFRACTION	30	CHAIN J AND (RESSEQ 280:349)

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