PDB-9k2n: Crystal structure of Glutamine Synthetase-apo

ID or keywords:

Entry

Database: PDB / ID: 9k2n

Title

Crystal structure of Glutamine Synthetase-apo

Components

Glutamine synthetase

Keywords

LIGASE / Acinetobacter baumannii / Glutamine synthetase / Biosynthetic protein

Function / homology

Function and homology information

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

Biological species

Acinetobacter baumannii AB0057 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.4 Å

Authors

Chandrasekaran, P. / Killivalavan, A. / Vaigundan, D. / Yuvaraj, I. / Manju, B. / Sekar, K.

Funding support

India, 1items

Citation

Journal: To Be Published
Title: Structure of glutamine synthetase from ESKAPE pathogen Acinetobacter baumannii
Authors: Chandrasekaran, P. / Killivalavan, A. / Vaigundan, D. / Yuvaraj, I. / Manju, B. / Sekar, K.

History

Deposition	Oct 17, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9k2n.cif.gz	2.4 MB	Display	PDBx/mmCIF format
PDB format	pdb9k2n.ent.gz		Display	PDB format
PDBx/mmJSON format	9k2n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9k2n_validation.pdf.gz	4.9 MB	Display	wwPDB validaton report
Full document	9k2n_full_validation.pdf.gz	5 MB	Display
Data in XML	9k2n_validation.xml.gz	116.7 KB	Display
Data in CIF	9k2n_validation.cif.gz	146.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k2/9k2n ftp://data.pdbj.org/pub/pdb/validation_reports/k2/9k2n	HTTPS FTP

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Related structure data

Similar structure data	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 (16)

Deposited unit

A: Glutamine synthetase

B: Glutamine synthetase

C: Glutamine synthetase

D: Glutamine synthetase

E: Glutamine synthetase

F: Glutamine synthetase

hetero molecules

314 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
Evidence: scanning transmission electron microscopy
628 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	260.909, 260.909, 154.18
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 469 / Label seq-ID: 1 - 468

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Glutamine synthetase Mass: 52130.668 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB0057 (bacteria) Gene: AB57_2783 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U3Y893, glutamine synthetase
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	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: 4.06 Å³/Da / Density % sol: 71.04 % / Description: Cuboid structure
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1M NaCl, 0.1M BICINE pH 9.0, 5mM MgCl2, 20% v/v polyethylene glycol monomethyl ether 550 PH range: 8.5 - 9.3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.4→99.59 Å / Num. obs: 72108 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC_1/2: 0.967 / Net I/σ(I): 9
Reflection shell	Resolution: 3.4→3.47 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4374 / CC_1/2: 0.36 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
autoPX	9.0.001	data processing
iMOSFLM	ccp4 9.0.001	data reduction
Aimless	ccp4 9.0.001	data scaling
MOLREP	ccp4 9.0.001	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.4→93.215 Å / Cor.coef. F_o:F_c: 0.904 / Cor.coef. F_o:F_c free: 0.881 / SU B: 77.444 / SU ML: 0.533 / Cross valid method: THROUGHOUT / ESU R Free: 0.532
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2702	3543	4.92 %	RANDOM
R_work	0.2327	68469	-	-
all	0.235	-	-	-
obs	-	72012	98.14 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 111.481 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.338 Å²	0 Å²	0 Å²
2-	-	-0.338 Å²	0 Å²
3-	-	-	0.676 Å²

Refinement step

Cycle: LAST / Resolution: 3.4→93.215 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21818	0	68	0	21886

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	22416
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	20468
X-RAY DIFFRACTION	r_angle_refined_deg	2.16	1.816	30374
X-RAY DIFFRACTION	r_angle_other_deg	0.73	1.757	47397
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.846	5	2802
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.384	5	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	23.761	10	3624
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.551	10	1050
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	3235
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	26510
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	5006
X-RAY DIFFRACTION	r_nbd_refined	0.246	0.2	5902
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.228	0.2	22538
X-RAY DIFFRACTION	r_nbtor_refined	0.2	0.2	11361
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	12624
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.154	0.2	786
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.043	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.232	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.26	0.2	142
X-RAY DIFFRACTION	r_nbd_other	0.274	0.2	418
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.284	0.2	24
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.051	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	4.721	3.007	11226
X-RAY DIFFRACTION	r_mcbond_other	4.721	3.007	11226
X-RAY DIFFRACTION	r_mcangle_it	7.949	5.39	14022
X-RAY DIFFRACTION	r_mcangle_other	7.948	5.389	14023
X-RAY DIFFRACTION	r_scbond_it	4.652	3.344	11190
X-RAY DIFFRACTION	r_scbond_other	4.652	3.344	11191
X-RAY DIFFRACTION	r_scangle_it	7.949	6.01	16352
X-RAY DIFFRACTION	r_scangle_other	7.949	6.01	16353
X-RAY DIFFRACTION	r_lrange_it	15.023	36.956	99077
X-RAY DIFFRACTION	r_lrange_other	15.022	36.955	99077
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.159	0.05	14717
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.174	0.05	14328
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.157	0.05	14620
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.168	0.05	14465
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.179	0.05	14179
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.172	0.05	14349
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.174	0.05	14453
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.178	0.05	14451
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.184	0.05	14230
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.175	0.05	14220
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.171	0.05	14529
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.169	0.05	14404
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.17	0.05	14448
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.178	0.05	14120
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.166	0.05	14560

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.15888	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.15888	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.17352	0.05007
2	4	C	X-RAY DIFFRACTION	Local ncs	0.17352	0.05007
3	5	A	X-RAY DIFFRACTION	Local ncs	0.15656	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.15656	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.16803	0.05007
4	8	E	X-RAY DIFFRACTION	Local ncs	0.16803	0.05007
5	9	A	X-RAY DIFFRACTION	Local ncs	0.17904	0.05007
5	10	F	X-RAY DIFFRACTION	Local ncs	0.17904	0.05007
6	11	B	X-RAY DIFFRACTION	Local ncs	0.17233	0.05007
6	12	C	X-RAY DIFFRACTION	Local ncs	0.17233	0.05007
7	13	B	X-RAY DIFFRACTION	Local ncs	0.17437	0.05007
7	14	D	X-RAY DIFFRACTION	Local ncs	0.17437	0.05007
8	15	B	X-RAY DIFFRACTION	Local ncs	0.17765	0.05007
8	16	E	X-RAY DIFFRACTION	Local ncs	0.17765	0.05007
9	17	B	X-RAY DIFFRACTION	Local ncs	0.18415	0.05007
9	18	F	X-RAY DIFFRACTION	Local ncs	0.18415	0.05007
10	19	C	X-RAY DIFFRACTION	Local ncs	0.17476	0.05007
10	20	D	X-RAY DIFFRACTION	Local ncs	0.17476	0.05007
11	21	C	X-RAY DIFFRACTION	Local ncs	0.17067	0.05007
11	22	E	X-RAY DIFFRACTION	Local ncs	0.17067	0.05007
12	23	C	X-RAY DIFFRACTION	Local ncs	0.16938	0.05007
12	24	F	X-RAY DIFFRACTION	Local ncs	0.16938	0.05007
13	25	D	X-RAY DIFFRACTION	Local ncs	0.16969	0.05007
13	26	E	X-RAY DIFFRACTION	Local ncs	0.16969	0.05007
14	27	D	X-RAY DIFFRACTION	Local ncs	0.17779	0.05007
14	28	F	X-RAY DIFFRACTION	Local ncs	0.17779	0.05007
15	29	E	X-RAY DIFFRACTION	Local ncs	0.16601	0.05007
15	30	F	X-RAY DIFFRACTION	Local ncs	0.16601	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.4-3.488	0.343	242	0.343	5001	0.343	5359	0.913	0.916	97.8354	0.317
3.488-3.584	0.321	262	0.287	4820	0.289	5204	0.932	0.947	97.6556	0.25
3.584-3.687	0.302	240	0.279	4722	0.28	5070	0.934	0.946	97.8698	0.239
3.687-3.801	0.274	239	0.25	4613	0.251	4920	0.952	0.96	98.6179	0.208
3.801-3.925	0.318	205	0.259	4527	0.261	4788	0.936	0.952	98.8304	0.222
3.925-4.063	0.279	239	0.233	4323	0.235	4631	0.951	0.965	98.51	0.193
4.063-4.216	0.272	235	0.22	4226	0.223	4496	0.954	0.97	99.2215	0.179
4.216-4.388	0.213	204	0.197	4045	0.198	4301	0.974	0.976	98.791	0.157
4.388-4.582	0.222	183	0.194	3914	0.195	4152	0.972	0.977	98.6753	0.151
4.582-4.805	0.245	230	0.197	3653	0.2	3968	0.97	0.977	97.8579	0.159
4.805-5.064	0.259	151	0.211	3556	0.213	3779	0.962	0.974	98.0947	0.172
5.064-5.371	0.232	193	0.196	3321	0.198	3574	0.97	0.977	98.3212	0.162
5.371-5.74	0.273	161	0.234	3176	0.236	3391	0.951	0.966	98.4075	0.197
5.74-6.198	0.328	167	0.238	2945	0.243	3166	0.927	0.965	98.2944	0.206
6.198-6.787	0.308	143	0.238	2731	0.241	2921	0.941	0.963	98.391	0.205
6.787-7.583	0.242	145	0.199	2460	0.202	2662	0.965	0.975	97.8587	0.176
7.583-8.746	0.22	100	0.2	2201	0.201	2372	0.97	0.974	97.0067	0.185
8.746-10.688	0.272	89	0.201	1882	0.204	2021	0.959	0.976	97.526	0.198
10.688-15.017	0.251	75	0.224	1485	0.225	1617	0.962	0.973	96.475	0.225
15.017-93.215	0.322	40	0.371	868	0.369	979	0.943	0.912	92.7477	0.463

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	3.1877	0.3205	0.269	1.3843	-0.2079	1.5916	-0.0507	0.141	-0.2343	0.0677	0.1187	-0.5757	0.0781	0.4498	-0.068	0.011	0.0314	-0.0504	0.1505	-0.0829	1.0321	95.672	-53.024	-33.1199
2	2.6375	0.9381	-0.0939	2.9745	0.9942	1.5162	-0.0177	-0.6772	0.5273	0.5559	-0.1044	-0.148	-0.1521	0.2982	0.1222	0.2458	-0.0352	-0.2149	0.2342	-0.1961	1.2133	78.1923	-18.0898	-13.8458
3	2.2826	0.3124	-0.2581	3.5991	0.0466	0.4786	-0.109	-0.1597	0.6762	0.05	-0.0325	0.414	-0.4805	-0.1239	0.1415	0.5637	0.1746	-0.3841	0.066	-0.2293	1.648	42.8365	0.9414	-31.273
4	2.2221	-0.0576	0.2169	2.3634	-0.941	1.5832	0.2491	-0.9182	-0.4176	0.9808	-0.0807	-0.2582	0.3252	-0.1092	-0.1684	0.8425	-0.1819	-0.3116	0.3873	0.1873	1.2562	68.88	-78.0603	-7.3731
5	0.7062	0.1025	-0.392	0.8938	-0.4853	3.6203	0.0543	-0.8997	0.2002	0.9204	-0.2254	0.1206	-0.0061	-0.3332	0.171	1.0214	-0.298	0.1225	1.3978	-0.3325	1.2239	49.8798	-43.0928	9.9816
6	2.2504	0.3898	-0.878	2.1006	0.2456	2.1791	0.0081	-0.7315	0.4878	0.697	-0.2757	0.9222	-0.3201	-0.784	0.2677	0.4617	0.1556	0.1612	0.9823	-0.7107	1.8994	14.867	-25.8694	-9.1554

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 503
2	X-RAY DIFFRACTION	2	ALL	B	2 - 502
3	X-RAY DIFFRACTION	3	ALL	C	2 - 501
4	X-RAY DIFFRACTION	4	ALL	D	2 - 501
5	X-RAY DIFFRACTION	5	ALL	E	2 - 501
6	X-RAY DIFFRACTION	6	ALL	F	2 - 501

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Mar 5, 2020. Novel coronavirus structure data

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Jul 12, 2017. Major update of PDB

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Yorodumi