PDB-3fky: Crystal structure of the glutamine synthetase Gln1deltaN18 from t...

ID or keywords:

Entry

Database: PDB / ID: 3fky

Title

Crystal structure of the glutamine synthetase Gln1deltaN18 from the yeast Saccharomyces cerevisiae

Components

Glutamine synthetase

Keywords

LIGASE / BETA-GRASP / CATALYTIC DOMAIN / Acetylation / Cytoplasm / Ubl conjugation

Function / homology

Function and homology information

Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / nuclear periphery / ATP binding / nucleus / cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

He, Y.X. / Gui, L. / Liu, Y.Z. / Du, Y. / Zhou, Y.Y. / Li, P. / Zhou, C.Z.

Citation

Journal: Proteins / Year: 2009
Title: Crystal structure of Saccharomyces cerevisiae glutamine synthetase Gln1 suggests a nanotube-like supramolecular assembly
Authors: He, Y.X. / Gui, L. / Liu, Y.Z. / Du, Y. / Zhou, Y. / Li, P. / Zhou, C.Z.

History

Deposition	Dec 18, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Oct 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _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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PDBx/mmCIF format	3fky.cif.gz	1.2 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	3fky_validation.pdf.gz	671.5 KB	Display	wwPDB validaton report
Full document	3fky_full_validation.pdf.gz	896.3 KB	Display
Data in XML	3fky_validation.xml.gz	250.3 KB	Display
Data in CIF	3fky_validation.cif.gz	322.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fk/3fky ftp://data.pdbj.org/pub/pdb/validation_reports/fk/3fky	HTTPS FTP

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Related structure data

Related structure data	2ojwS S: Starting model for refinement
Similar structure data	7at1-1 1acm-1 4bax-d 1at1-1 2a0f-1 2at1-1 4kh1-1 1f1b-1 Search similar-shape structures by Omokage search (details) 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) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#30 - Jun 2002
Glutamine Synthetase
similarity (12)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

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

K: Glutamine synthetase

L: Glutamine synthetase

M: Glutamine synthetase

N: Glutamine synthetase

O: Glutamine synthetase

P: Glutamine synthetase

Q: Glutamine synthetase

R: Glutamine synthetase

S: Glutamine synthetase

T: Glutamine synthetase

hetero molecules

839 kDa, 20 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

G: Glutamine synthetase

H: Glutamine synthetase

I: Glutamine synthetase

J: Glutamine synthetase

hetero molecules

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

2

K: Glutamine synthetase

L: Glutamine synthetase

M: Glutamine synthetase

N: Glutamine synthetase

O: Glutamine synthetase

P: Glutamine synthetase

Q: Glutamine synthetase

R: Glutamine synthetase

S: Glutamine synthetase

T: Glutamine synthetase

hetero molecules

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

Unit cell

Length a, b, c (Å)	128.650, 129.940, 135.610
Angle α, β, γ (deg.)	93.46, 104.61, 104.01
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Ens-ID: 1

Dom-ID	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	1	ARG	ARG	HIS	HIS	A	A	21 - 70	21 - 70
1	2	ASP	ASP	ARG	ARG	A	A	73 - 292	73 - 292
1	3	SER	SER	GLU	GLU	A	A	301 - 366	301 - 366
2	1	ARG	ARG	HIS	HIS	B	B	21 - 70	21 - 70
2	2	ASP	ASP	ARG	ARG	B	B	73 - 292	73 - 292
2	3	SER	SER	GLU	GLU	B	B	301 - 366	301 - 366
3	1	ARG	ARG	HIS	HIS	C	C	21 - 70	21 - 70
3	2	ASP	ASP	ARG	ARG	C	C	73 - 292	73 - 292
3	3	SER	SER	GLU	GLU	C	C	301 - 366	301 - 366
4	1	ARG	ARG	HIS	HIS	D	D	21 - 70	21 - 70
4	2	ASP	ASP	ARG	ARG	D	D	73 - 292	73 - 292
4	3	SER	SER	GLU	GLU	D	D	301 - 366	301 - 366
5	1	ARG	ARG	HIS	HIS	E	E	21 - 70	21 - 70
5	2	ASP	ASP	ARG	ARG	E	E	73 - 292	73 - 292
5	3	SER	SER	GLU	GLU	E	E	301 - 366	301 - 366
6	1	ARG	ARG	HIS	HIS	F	F	21 - 70	21 - 70
6	2	ASP	ASP	ARG	ARG	F	F	73 - 292	73 - 292
6	3	SER	SER	GLU	GLU	F	F	301 - 366	301 - 366
7	1	ARG	ARG	HIS	HIS	G	G	21 - 70	21 - 70
7	2	ASP	ASP	ARG	ARG	G	G	73 - 292	73 - 292
7	3	SER	SER	GLU	GLU	G	G	301 - 366	301 - 366
8	1	ARG	ARG	HIS	HIS	H	H	21 - 70	21 - 70
8	2	ASP	ASP	ARG	ARG	H	H	73 - 292	73 - 292
8	3	SER	SER	GLU	GLU	H	H	301 - 366	301 - 366
9	1	ARG	ARG	HIS	HIS	I	I	21 - 70	21 - 70
9	2	ASP	ASP	ARG	ARG	I	I	73 - 292	73 - 292
9	3	SER	SER	GLU	GLU	I	I	301 - 366	301 - 366
10	1	ARG	ARG	HIS	HIS	J	J	21 - 70	21 - 70
10	2	ASP	ASP	ARG	ARG	J	J	73 - 292	73 - 292
10	3	SER	SER	GLU	GLU	J	J	301 - 366	301 - 366
11	1	ARG	ARG	HIS	HIS	K	K	21 - 70	21 - 70
11	2	ASP	ASP	ARG	ARG	K	K	73 - 292	73 - 292
11	3	SER	SER	GLU	GLU	K	K	301 - 366	301 - 366
12	1	ARG	ARG	HIS	HIS	L	L	21 - 70	21 - 70
12	2	ASP	ASP	ARG	ARG	L	L	73 - 292	73 - 292
12	3	SER	SER	GLU	GLU	L	L	301 - 366	301 - 366
13	1	ARG	ARG	HIS	HIS	M	M	21 - 70	21 - 70
13	2	ASP	ASP	ARG	ARG	M	M	73 - 292	73 - 292
13	3	SER	SER	GLU	GLU	M	M	301 - 366	301 - 366
14	1	ARG	ARG	HIS	HIS	N	N	21 - 70	21 - 70
14	2	ASP	ASP	ARG	ARG	N	N	73 - 292	73 - 292
14	3	SER	SER	GLU	GLU	N	N	301 - 366	301 - 366
15	1	ARG	ARG	HIS	HIS	O	O	21 - 70	21 - 70
15	2	ASP	ASP	ARG	ARG	O	O	73 - 292	73 - 292
15	3	SER	SER	GLU	GLU	O	O	301 - 366	301 - 366
16	1	ARG	ARG	HIS	HIS	P	P	21 - 70	21 - 70
16	2	ASP	ASP	ARG	ARG	P	P	73 - 292	73 - 292
16	3	SER	SER	GLU	GLU	P	P	301 - 366	301 - 366
17	1	ARG	ARG	HIS	HIS	Q	Q	21 - 70	21 - 70
17	2	ASP	ASP	ARG	ARG	Q	Q	73 - 292	73 - 292
17	3	SER	SER	GLU	GLU	Q	Q	301 - 366	301 - 366
18	1	ARG	ARG	HIS	HIS	R	R	21 - 70	21 - 70
18	2	ASP	ASP	ARG	ARG	R	R	73 - 292	73 - 292
18	3	SER	SER	GLU	GLU	R	R	301 - 366	301 - 366
19	1	ARG	ARG	HIS	HIS	S	S	21 - 70	21 - 70
19	2	ASP	ASP	ARG	ARG	S	S	73 - 292	73 - 292
19	3	SER	SER	GLU	GLU	S	S	301 - 366	301 - 366
20	1	ARG	ARG	HIS	HIS	T	T	21 - 70	21 - 70
20	2	ASP	ASP	ARG	ARG	T	T	73 - 292	73 - 292
20	3	SER	SER	GLU	GLU	T	T	301 - 366	301 - 366

#1: Protein	Glutamine synthetase / GS / Glutamate--ammonia ligase Mass: 41759.863 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: GLN1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P32288, glutamine synthetase
#2: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₆H₅O₇
Sequence details	THESE SEQUENCE APPEARES IN REFERENCE 2 IN UNP DATABASE, P32288.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.53 Å³/Da / Density % sol: 51.33 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M sodium acetate, 0.1M sodium citrate, 8% polyethylene glycol 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.95→65.25 Å / Num. obs: 163752 / % possible obs: 95.1 % / Redundancy: 2.1 % / B_iso Wilson estimate: 48.67 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 7.9
Reflection shell	Resolution: 2.95→3.11 Å / Redundancy: 2 % / R_merge(I) obs: 0.407 / Mean I/σ(I) obs: 2.1 / Num. unique all: 23325 / % possible all: 92.9

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
MOLREP		phasing
PHENIX	(phenix.refine)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OJW

2ojw

Resolution: 2.95→65.218 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.817 / SU ML: 0.47 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 26.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.258	6055	2.02 %	RANDOM
R_work	0.225	293890	-	-
obs	0.226	163752	87.12 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.96 Å² / k_sol: 0.388 e/Å³

Displacement parameters

B_iso max: 146.1 Å² / B_iso mean: 47.505 Å² / B_iso min: 9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.313 Å²	2.906 Å²	-2.991 Å²
2-	-	-7.23 Å²	-3.638 Å²
3-	-	-	6.918 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→65.218 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	53258	0	260	0	53518

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	54939
X-RAY DIFFRACTION	f_angle_d	1.24	74295
X-RAY DIFFRACTION	f_chiral_restr	0.08	7387
X-RAY DIFFRACTION	f_plane_restr	0.005	9828
X-RAY DIFFRACTION	f_dihedral_angle_d	20.149	19753

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2661	X-RAY DIFFRACTION	POSITIONAL
1	2	B	2661	X-RAY DIFFRACTION	POSITIONAL	0.053
1	3	C	2661	X-RAY DIFFRACTION	POSITIONAL	0.059
1	4	D	2661	X-RAY DIFFRACTION	POSITIONAL	0.053
1	5	E	2661	X-RAY DIFFRACTION	POSITIONAL	0.053
1	6	F	2661	X-RAY DIFFRACTION	POSITIONAL	0.05
1	7	G	2661	X-RAY DIFFRACTION	POSITIONAL	0.057
1	8	H	2661	X-RAY DIFFRACTION	POSITIONAL	0.056
1	9	I	2661	X-RAY DIFFRACTION	POSITIONAL	0.058
1	10	J	2661	X-RAY DIFFRACTION	POSITIONAL	0.056
1	11	K	2661	X-RAY DIFFRACTION	POSITIONAL	0.056
1	12	L	2661	X-RAY DIFFRACTION	POSITIONAL	0.053
1	13	M	2661	X-RAY DIFFRACTION	POSITIONAL	0.054
1	14	N	2661	X-RAY DIFFRACTION	POSITIONAL	0.053
1	15	O	2661	X-RAY DIFFRACTION	POSITIONAL	0.054
1	16	P	2661	X-RAY DIFFRACTION	POSITIONAL	0.052
1	17	Q	2661	X-RAY DIFFRACTION	POSITIONAL	0.054
1	18	R	2661	X-RAY DIFFRACTION	POSITIONAL	0.054
1	19	S	2661	X-RAY DIFFRACTION	POSITIONAL	0.052
1	20	T	2661	X-RAY DIFFRACTION	POSITIONAL	0.051

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.95-2.984	0.366	179	0.35	8746	8925	78
2.984-3.019	0.404	168	0.33	8794	8962	78
3.019-3.055	0.343	238	0.319	8866	9104	80
3.055-3.094	0.357	183	0.31	8945	9128	79
3.094-3.135	0.329	169	0.308	9259	9428	82
3.135-3.178	0.376	162	0.297	9211	9373	82
3.178-3.223	0.26	188	0.276	9355	9543	83
3.223-3.271	0.311	210	0.283	9312	9522	84
3.271-3.322	0.313	211	0.278	9579	9790	84
3.322-3.377	0.284	225	0.26	9642	9867	86
3.377-3.435	0.292	174	0.262	9670	9844	86
3.435-3.497	0.308	188	0.271	9755	9943	87
3.497-3.565	0.33	194	0.253	9841	10035	87
3.565-3.638	0.304	179	0.23	9787	9966	87
3.638-3.717	0.262	183	0.23	9952	10135	88
3.717-3.803	0.269	213	0.228	9905	10118	88
3.803-3.898	0.243	230	0.213	9940	10170	89
3.898-4.004	0.227	200	0.208	9991	10191	89
4.004-4.121	0.227	213	0.194	10022	10235	89
4.121-4.254	0.211	238	0.197	9983	10221	89
4.254-4.406	0.231	199	0.188	10101	10300	90
4.406-4.583	0.196	196	0.179	10141	10337	90
4.583-4.791	0.205	197	0.175	10182	10379	90
4.791-5.044	0.238	235	0.171	10212	10447	91
5.044-5.36	0.217	215	0.17	10344	10559	91
5.36-5.773	0.176	196	0.169	10280	10476	92
5.773-6.354	0.22	226	0.193	10347	10573	92
6.354-7.272	0.232	213	0.199	10514	10727	93
7.272-9.158	0.202	261	0.176	10546	10807	94
9.158-65.234	0.245	172	0.238	10668	10840	95

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