PDB-4s17: The crystal structure of glutamine synthetase from Bifidobacteriu...

ID or keywords:

Entry

Database: PDB / ID: 4s17

Title

The crystal structure of glutamine synthetase from Bifidobacterium adolescentis ATCC 15703

Components

Glutamine synthetase

Keywords

LIGASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

Function and homology information

nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / membrane / cytoplasm
Similarity search - Function

Biological species

Bifidobacterium adolescentis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Cuff, M. / Tan, K. / Mack, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of glutamine synthetase from Bifidobacterium adolescentis ATCC 15703
Authors: Cuff, M. / Tan, K. / Mack, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Jan 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 28, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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	4s17.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb4s17.ent.gz	865.1 KB	Display	PDB format
PDBx/mmJSON format	4s17.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/s1/4s17 ftp://data.pdbj.org/pub/pdb/validation_reports/s1/4s17	HTTPS FTP

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Related structure data

Similar structure data	1lgr-d 2wgs-d 20334 2lgs-d 3ng0-1 4xyc-2 5zlp-d 1f1h-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC110218

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#30 - Jun 2002 Glutamine Synthetase similarity (13)

Deposited unit

A: Glutamine synthetase

B: Glutamine synthetase

C: Glutamine synthetase

D: Glutamine synthetase

E: Glutamine synthetase

F: Glutamine synthetase

hetero molecules

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

1

A: Glutamine synthetase

B: Glutamine synthetase

C: Glutamine synthetase

D: Glutamine synthetase

E: Glutamine synthetase

F: Glutamine synthetase

hetero molecules

A: Glutamine synthetase

B: Glutamine synthetase

C: Glutamine synthetase

D: Glutamine synthetase

E: Glutamine synthetase

F: Glutamine synthetase

hetero molecules

defined by author&software
646 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.052, 134.052, 298.915
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Details

Experimentally unknown. It is predicted to be dodecamer.

#1: Protein	Glutamine synthetase Mass: 53782.500 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium adolescentis (bacteria) Strain: ATCC 15703 / Gene: BAD_0943, glnA1 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: A1A1Z1, glutamine synthetase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.8 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M MgCl2, 0.1M HEPES:NaOH, 30% (v/v) PPG P400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2013 / Details: mirror
Radiation	Monochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.3→45.8 Å / Num. all: 137577 / Num. obs: 137577 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 7.5 % / B_iso Wilson estimate: 27.2 Å² / R_merge(I) obs: 0.112 / Net I/σ(I): 14.9
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.741 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6832 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD	Builder/HKL3000	phasing
MLPHARE	Builder/HKL3000	phasing
DM	Builder/HKL3000	model building
DENZO	Builder/HKL3000	data reduction
SCALEPACK	Builder/HKL3000	data scaling
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM	Builder/HKL3000	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→45.78 Å / SU ML: 0.38 / σ(F): 1.33 / Phase error: 30.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2874	6708	4.93 %	randon
R_work	0.2385	-	-	-
obs	0.2409	136042	98.71 %	-
all	-	136042	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→45.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20833	0	14	412	21259

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	21364
X-RAY DIFFRACTION	f_angle_d	0.588	29015
X-RAY DIFFRACTION	f_dihedral_angle_d	11.394	7681
X-RAY DIFFRACTION	f_chiral_restr	0.041	3169
X-RAY DIFFRACTION	f_plane_restr	0.003	3826

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 (%)
2.3043-2.3305	0.3414	203	0.3095	3902	X-RAY DIFFRACTION	91
2.3305-2.3579	0.3773	201	0.3097	4097	X-RAY DIFFRACTION	94
2.3579-2.3866	0.3848	245	0.3266	4058	X-RAY DIFFRACTION	96
2.3866-2.4168	0.363	219	0.309	4204	X-RAY DIFFRACTION	97
2.4168-2.4486	0.3931	250	0.3126	4233	X-RAY DIFFRACTION	98
2.4486-2.4822	0.3899	224	0.3067	4279	X-RAY DIFFRACTION	98
2.4822-2.5176	0.4142	226	0.3001	4234	X-RAY DIFFRACTION	99
2.5176-2.5552	0.37	223	0.2981	4303	X-RAY DIFFRACTION	100
2.5552-2.5951	0.3474	208	0.3018	4315	X-RAY DIFFRACTION	99
2.5951-2.6377	0.3564	227	0.2899	4344	X-RAY DIFFRACTION	100
2.6377-2.6831	0.3679	191	0.2933	4384	X-RAY DIFFRACTION	100
2.6831-2.7319	0.3411	236	0.2899	4307	X-RAY DIFFRACTION	100
2.7319-2.7845	0.3555	213	0.2964	4297	X-RAY DIFFRACTION	100
2.7845-2.8413	0.35	229	0.2966	4318	X-RAY DIFFRACTION	100
2.8413-2.9031	0.325	220	0.2856	4339	X-RAY DIFFRACTION	100
2.9031-2.9706	0.3265	243	0.2779	4316	X-RAY DIFFRACTION	100
2.9706-3.0449	0.3304	219	0.2651	4327	X-RAY DIFFRACTION	100
3.0449-3.1272	0.3283	207	0.2725	4355	X-RAY DIFFRACTION	100
3.1272-3.2192	0.2958	188	0.2692	4384	X-RAY DIFFRACTION	100
3.2192-3.323	0.3207	212	0.2649	4350	X-RAY DIFFRACTION	100
3.323-3.4418	0.2818	233	0.2395	4349	X-RAY DIFFRACTION	99
3.4418-3.5795	0.2742	255	0.2335	4301	X-RAY DIFFRACTION	100
3.5795-3.7424	0.2668	255	0.2214	4360	X-RAY DIFFRACTION	100
3.7424-3.9396	0.25	233	0.2034	4365	X-RAY DIFFRACTION	100
3.9396-4.1862	0.2414	235	0.1953	4359	X-RAY DIFFRACTION	99
4.1862-4.5092	0.2101	216	0.1809	4372	X-RAY DIFFRACTION	99
4.5092-4.9625	0.1963	219	0.1669	4417	X-RAY DIFFRACTION	99
4.9625-5.6794	0.2395	196	0.1755	4456	X-RAY DIFFRACTION	100
5.6794-7.1511	0.2238	249	0.1845	4455	X-RAY DIFFRACTION	99
7.1511-45.7907	0.2189	233	0.1908	4554	X-RAY DIFFRACTION	97

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	2.2194	-0.3953	-0.6495	2.3106	-1.6457	1.5735	-0.0839	-0.2131	-0.3859	0.2506	-0.0395	-0.1464	0.2579	0.2357	0.1121	0.5541	0.1713	-0.0446	0.2448	0.0522	0.3611	37.8652	-51.2585	84.8345
2	0.4854	0.0931	-0.0109	0.4119	0.0585	0.4223	-0.0076	0.0313	-0.0269	0.1168	-0.044	-0.0933	-0.0932	0.0831	0.0472	0.4726	0.1861	-0.0317	0.2462	0.0239	0.2768	44.0331	-33.4683	72.588
3	0.737	-0.3933	0.4337	0.518	-0.2511	0.612	-0.021	-0.0287	-0.0501	0.0511	0.0572	-0.2545	0.0071	0.2581	0.0183	0.4807	0.1968	-0.048	0.3334	-0.006	0.4079	59.9814	-41.0998	64.6635
4	1.3937	0.6828	-0.2955	1.2919	-0.5247	1.005	-0.0273	-0.1179	-0.1744	0.1922	-0.1144	-0.2873	-0.0361	0.2468	0.1159	0.5154	0.1017	-0.0747	0.2416	-0.001	0.2983	55.2737	-8.3581	79.7022
5	0.6921	-0.3842	-0.0065	0.2801	-0.1902	0.5872	-0.0494	-0.0273	0.1808	0.1481	0.0326	-0.0685	-0.2912	-0.0598	0.0368	0.569	0.1374	-0.0291	0.2133	0.0216	0.2781	38.1902	5.5675	69.1091
6	1.2012	0.9224	1.4458	0.7165	1.1879	2.5145	-0.0124	0.0746	0.2016	-0.0308	-0.1137	-0.0626	-0.2073	0.0899	0.1191	0.4481	0.0965	0.0186	0.2293	0.0431	0.3307	57.0043	10.2475	60.2784
7	0.8263	-0.8074	-0.0861	1.7145	0.0898	0.0107	-0.0276	-0.0465	0.2401	0.0538	0.0232	-0.2216	-0.1311	0.0118	-0.0925	0.8072	0.2021	-0.0678	0.2457	-0.0805	0.3335	26.9632	23.4963	81.1769
8	0.2944	0.0077	0.0506	0.2777	-0.1875	0.1342	-0.014	-0.0216	0.0805	0.1552	-0.0149	0.0404	-0.1168	-0.0398	-0.0196	0.7366	0.2637	0.0079	0.2047	0.0287	0.297	4.9758	14.8425	70.6807
9	0.0924	-0.1118	-0.0699	0.8009	0.4199	0.2462	-0.1088	-0.0512	0.0988	0.0493	-0.0342	0.0883	-0.1818	-0.0734	-0.0002	0.8022	0.2922	-0.0062	0.2788	0.0154	0.3769	9.3686	34.7558	62.8182
10	1.1047	-0.6577	0.0517	1.238	0.3578	0.3276	0.0158	0.0185	0.218	-0.0263	-0.061	0.0131	-0.1125	-0.0883	-0.0079	0.8026	0.2337	0.0693	0.2692	-0.0059	0.2895	-11.1052	15.2155	84.7588
11	0.2565	-0.1968	0.0122	0.6178	0.0626	0.2295	-0.0138	0.0278	-0.0919	0.2736	0.0049	0.1893	-0.05	-0.0663	0.0492	0.6665	0.2684	0.0945	0.25	-0.0121	0.3014	-21.7694	-5.861	75.0277
12	0.588	-0.3068	-0.6304	0.2811	0.4342	1.1161	-0.0638	0.0711	-0.0818	0.0958	-0.0964	0.2438	-0.0001	-0.2196	0.1625	0.6754	0.2941	0.104	0.3833	-0.0278	0.4081	-35.4082	5.392	67.3268
13	1.9741	0.4993	0.4225	2.8759	2.0188	2.4457	0.0501	-0.2393	0.1749	0.1167	-0.192	0.2911	-0.1291	-0.3338	0.1574	0.6201	0.1396	0.0813	0.2706	-0.0156	0.2656	-25.4352	-21.0757	89.4882
14	1.3609	0.6995	-0.1309	1.4986	0.5686	0.5535	0.0829	0.0395	0.1632	0.0841	-0.1093	0.3175	-0.1706	-0.2231	0.1041	0.5424	0.2101	0.1237	0.322	-0.0279	0.2706	-31.3285	-28.7497	85.7884
15	0.6135	-0.1136	-0.2361	0.4749	0.2652	0.521	0.0135	-0.003	-0.0774	0.1602	-0.0025	-0.0472	0.0407	-0.0286	0.0247	0.5354	0.1641	0.0425	0.2166	0.0001	0.2709	-13.1361	-42.3831	75.38
16	0.9583	0.9247	-1.2875	0.915	-1.1223	2.9323	0.01	0.0737	-0.191	0.0719	-0.08	0.0318	0.1888	-0.2148	0.0857	0.4309	0.1061	0.0252	0.2647	-0.0205	0.2932	-32.2546	-47.8583	69.4199
17	1.9027	0.1487	-0.4641	3.7051	0.3129	1.1859	-0.0777	-0.1784	-0.2429	0.1744	0.0201	0.0784	0.1646	-0.0983	0.0297	0.5386	0.1224	0.059	0.215	0.0667	0.2704	-1.8834	-55.423	87.3593
18	0.5334	0.1636	-0.0859	0.6675	-0.0244	0.3438	0.0156	-0.0505	-0.1249	0.1832	-0.0312	-0.1141	0.0805	0.0597	0.0264	0.5308	0.182	-0.0032	0.2586	0.0158	0.2984	19.9089	-55.1165	74.3049
19	0.1571	-0.3056	0.2867	0.9962	-0.8359	0.726	-0.051	0.0464	-0.1186	0.0398	-0.1243	-0.087	0.1517	0.1171	0.11	0.6066	0.1662	0.0707	0.2183	0.0077	0.3963	15.5306	-72.0394	67.0113

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 257 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 258 through 478 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 140 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 141 through 300 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 301 through 478 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 3 through 135 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 136 through 300 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 301 through 478 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 3 through 108 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 109 through 300 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 301 through 478 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 4 through 58 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 59 through 123 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 124 through 300 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 301 through 478 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 4 through 108 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 109 through 300 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 301 through 478 )

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