PDB-2ojw: Crystal structure of human glutamine synthetase in complex with A...

ID or keywords:

Entry

Database: PDB / ID: 2ojw

Title

Crystal structure of human glutamine synthetase in complex with ADP and phosphate

Components

Glutamine synthetase

Keywords

LIGASE / AMINO-ACID BIOSYNTHESIS / SYNTHETASE /

STRUCTURAL GENOMICS /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

protein S-acyltransferase / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus /

regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamate catabolic process /

glutamine synthetase / glutamine biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Karlberg, T. / Uppenberg, J. / Arrowsmith, C. / Berglund, H. / Busam, R.D. / Collins, R. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. ...

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design.
Authors: Krajewski, W.W. / Collins, R. / Holmberg-Schiavone, L. / Jones, T.A. / Karlberg, T. / Mowbray, S.L.

History

Deposition	Jan 15, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2007	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2007	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.3	Aug 30, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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	2ojw.cif.gz	408.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2ojw.ent.gz	325.5 KB	Display	PDB format
PDBx/mmJSON format	2ojw.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/oj/2ojw ftp://data.pdbj.org/pub/pdb/validation_reports/oj/2ojw	HTTPS FTP

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Related structure data

Related structure data	2qc8C 2uu7C 2d3aS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2uu7-2 2uu7-1 5fv4-d 2qc8-d 1v3c-2 6ncz-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

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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

hetero molecules

221 kDa, 5 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

hetero molecules

A: Glutamine synthetase

B: Glutamine synthetase

C: Glutamine synthetase

D: Glutamine synthetase

E: Glutamine synthetase

hetero molecules

defined by author&software
443 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	177.600, 122.600, 126.600
Angle α, β, γ (deg.)	90.00, 130.60, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain: (Details: A B C D E)
NCS domain segments:

Dom-ID: 1 / Ens-ID: 1 / Refine code: 5

Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	MET	MET	ASN	ASN	A	A	18 - 310	37 - 329
2	MET	MET	ASN	ASN	B	B	18 - 310	37 - 329
3	MET	MET	ASN	ASN	C	C	18 - 310	37 - 329
4	MET	MET	ASN	ASN	D	D	18 - 310	37 - 329
5	MET	MET	ASN	ASN	E	E	18 - 310	37 - 329
6	ALA	ALA	GLY	GLY	A	A	317 - 365	336 - 384
7	ALA	ALA	GLY	GLY	B	B	317 - 365	336 - 384
8	ALA	ALA	GLY	GLY	C	C	317 - 365	336 - 384
9	ALA	ALA	GLY	GLY	D	D	317 - 365	336 - 384
10	ALA	ALA	THR	THR	E	E	317 - 364	336 - 383

Details

The biological assembly is a decamer generated from the pentamer in the asymmetric unit by the operation: -x, y, -z

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Protein , 1 types, 5 molecules ABCDE

#1: Protein	Glutamine synthetase / / Glutamate-ammonia ligase / GS Mass: 43364.773 Da / Num. of mol.: 5 / Fragment: Residues 4-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLUL, GLNS / Plasmid: PNIC-BSA4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15104, glutamine synthetase

#1: Protein

Glutamine synthetase /

/ Glutamate-ammonia ligase / GS

Mass: 43364.773 Da / Num. of mol.: 5 / Fragment: Residues 4-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: GLUL, GLNS / Plasmid: PNIC-BSA4 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15104,

glutamine synthetase

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Non-polymers , 6 types, 1431 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1390 / 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: 2.41 Å³/Da / Density % sol: 49 %
Crystal grow	Temperature: 277 K / pH: 7.5 Details: 10% Isopropanol, 200 mM NaCl, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2006 / Details: FOCUSING: TOROIDAL MIRROR
Radiation	Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.05→40 Å / Num. obs: 125431 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / R_merge(I) obs: 0.1205 / R_sym value: 0.14
Reflection shell	Resolution: 2.05→2.15 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.416 / R_sym value: 0.485 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
REFMAC	5.3.0021	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D3A

2d3a

Resolution: 2.05→39.25 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.92 / SU B: 7.039 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	6388	5 %	RANDOM
R_work	0.159	-	-	-
obs	0.162	121373	100 %	-
all	-	121373	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 11.84 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.15 Å²	0 Å²	1.01 Å²
2-	-	0.13 Å²	0 Å²
3-	-	-	1.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→39.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14250	0	221	1390	15861

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	14840
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10359
X-RAY DIFFRACTION	r_angle_refined_deg	1.776	1.958	20083
X-RAY DIFFRACTION	r_angle_other_deg	1.094	3	24991
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	12.756	5	1796
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.81	23.388	729
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.792	15	2414
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.345	15	122
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	2023
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	16607
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3167
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	2676
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	10497
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	6671
X-RAY DIFFRACTION	r_nbtor_other	0.084	0.2	7178
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	1047
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.182	0.2	24
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.195	0.2	77
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.234	0.2	14
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.096	1.5	11515
X-RAY DIFFRACTION	r_mcbond_other	0.244	1.5	3658
X-RAY DIFFRACTION	r_mcangle_it	1.301	2	14361
X-RAY DIFFRACTION	r_scbond_it	2.203	3	7035
X-RAY DIFFRACTION	r_scangle_it	3.051	4.5	5719
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	1940	medium positional	0.15	0.5
B	1940	medium positional	0.13	0
C	1940	medium positional	0.13	0
D	1940	medium positional	0.14	0
E	1940	medium positional	0.15	0
A	2571	loose positional	0.46	5
B	2571	loose positional	0.45	0
C	2571	loose positional	0.45	0
D	2571	loose positional	0.44	0
E	2571	loose positional	0.44	0
A	1940	medium thermal	0.87	2
B	1940	medium thermal	0.68	0
C	1940	medium thermal	0.61	0
D	1940	medium thermal	0.58	0
E	1940	medium thermal	0.79	0
A	2571	loose thermal	0.89	10
B	2571	loose thermal	0.78	0
C	2571	loose thermal	0.82	0
D	2571	loose thermal	0.78	0
E	2571	loose thermal	0.83	0

LS refinement shell

Resolution: 2.05→2.1 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.289	468	-
R_work	0.198	8909	-
obs	-	-	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	0.3781	-0.2948	-0.1802	0.4079	0.1315	0.1311	-0.0136	-0.002	0.059	-0.0562	0.0122	-0.0337	-0.0269	0.0263	0.0015	-0.0218	0.0028	0.0129	0.0321	0.0084	-0.0564	20.097	17.921	-36.119
2	0.0185	0.0439	-0.0569	0.2633	-0.1731	0.1844	0.0243	0.0202	-0.0404	0.046	-0.0154	0.0091	0.0276	0.0237	-0.0089	-0.0166	0.0043	-0.0003	0.0396	-0.0102	-0.0592	19.254	-3.839	-26.583
3	0.2571	-0.1111	-0.1498	0.3035	0.0639	0.3167	0.0091	-0.003	-0.0199	-0.014	-0.0018	-0.0028	0.0143	-0.0275	-0.0073	-0.0249	0.0076	0.0097	0.0115	-0.0045	-0.0566	24.45	-6.883	-31.949
4	0.5337	0.0154	-0.183	0.2425	0.0912	0.1155	0.0127	0.0419	0.0658	-0.0615	-0.0262	0.009	-0.0088	-0.0255	0.0135	-0.0169	-0.0082	-0.021	-0.0052	0.0402	-0.0272	-4.519	43.378	-28.606
5	0.2717	-0.0925	0.068	0.4343	-0.1235	0.171	-0.0394	-0.0051	0.0453	0.0065	0.0442	-0.031	0.0064	0.0252	-0.0048	-0.025	0.0014	-0.0012	0.0242	0.001	-0.0311	16.892	33.185	-25.955
6	0.3883	0.0112	-0.1807	0.3221	-0.056	0.4896	0.0064	0.0056	0.0791	-0.0269	0.0459	-0.0535	0.0161	0.0805	-0.0523	-0.0369	-0.0115	0.0085	0.0169	-0.0005	-0.0086	20.479	38.393	-30.945
7	0.1934	0.0153	0.021	0.5267	-0.1884	0.071	-0.0346	0.024	0.0434	-0.0211	0.0264	0.0493	0.0193	-0.0299	0.0083	-0.045	0.0037	-0.036	0.0124	0.0039	-0.0093	-34.796	26.742	-18.196
8	0.628	0.0851	0.3344	0.1937	0.0947	0.2841	0.0017	-0.0959	0.0876	-0.0225	-0.0124	0.0117	0.0106	-0.0331	0.0107	-0.0408	-0.0008	-0.0146	0.0121	-0.0003	-0.0159	-17.191	42.191	-14.859
9	0.3925	-0.0134	0.1862	0.3162	0.0024	0.2	-0.0313	-0.0285	0.0994	-0.0373	0.0035	0.0475	0.0084	-0.0028	0.0278	-0.0567	0.0103	-0.0189	-0.0069	0.0043	0.0189	-21.505	48.463	-17.248
10	0.7508	-0.1857	-0.0946	0.3053	0.0771	0.023	-0.0019	0.0547	-0.0986	-0.0369	-0.0217	0.0688	0.0197	-0.0121	0.0236	-0.0336	-0.038	-0.0079	0.0194	-0.0312	-0.0087	-29.343	-8.905	-20.374
11	0.4292	0.1677	-0.0045	0.5658	0.1727	0.0609	-0.0164	0.006	-0.0202	0.0396	-0.0194	0.0275	-0.0133	-0.0069	0.0358	-0.0271	-0.0189	-0.0078	0.0104	-0.009	-0.0176	-36.008	10.934	-8.847
12	0.4714	-0.0955	0.0407	0.3507	0.2001	0.1699	-0.0005	0.025	-0.0389	0.025	-0.0508	0.0868	-0.0039	-0.0021	0.0514	-0.0538	-0.0325	0.0005	0.0056	-0.0152	0.0087	-43.762	9.507	-10.148
13	0.408	0.0491	-0.1319	0.4261	0.0603	0.1562	-0.0124	0.1128	-0.0514	-0.0137	-0.0233	0.0257	0.0439	0.0324	0.0356	-0.0013	0.0039	0.0046	0.0189	-0.0404	-0.0485	4.672	-14.571	-31.856
14	0.5126	-0.1326	-0.2773	0.0362	0.0498	0.4101	-0.0443	-0.0258	-0.0555	0.0303	-0.0122	0.0523	0.0822	-0.0046	0.0566	0.0132	-0.0178	0.0149	0.0129	-0.0066	-0.0306	-13.405	-17.631	-16.339
15	0.4787	0.0835	-0.0976	0.3626	0.0768	0.3435	-0.0465	0.0161	-0.1393	0.0107	0.0093	0.03	0.0577	-0.0307	0.0372	0.0011	-0.018	0.0185	-0.0047	-0.0343	0.0083	-15.456	-24.68	-19.639

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	11 - 127	30 - 146
2	X-RAY DIFFRACTION	2	A	A	128 - 177	147 - 196
3	X-RAY DIFFRACTION	3	A	A	178 - 365	197 - 384
4	X-RAY DIFFRACTION	4	B	B	13 - 127	32 - 146
5	X-RAY DIFFRACTION	5	B	B	128 - 177	147 - 196
6	X-RAY DIFFRACTION	6	B	B	178 - 365	197 - 384
7	X-RAY DIFFRACTION	7	C	C	10 - 127	29 - 146
8	X-RAY DIFFRACTION	8	C	C	128 - 177	147 - 196
9	X-RAY DIFFRACTION	9	C	C	178 - 365	197 - 384
10	X-RAY DIFFRACTION	10	D	D	11 - 127	30 - 146
11	X-RAY DIFFRACTION	11	D	D	128 - 177	147 - 196
12	X-RAY DIFFRACTION	12	D	D	178 - 365	197 - 384
13	X-RAY DIFFRACTION	13	E	E	15 - 127	34 - 146
14	X-RAY DIFFRACTION	14	E	E	128 - 177	147 - 196
15	X-RAY DIFFRACTION	15	E	E	178 - 364	197 - 383

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